diff --git a/.agents/skills/filigree-workflow/SKILL.md b/.agents/skills/filigree-workflow/SKILL.md new file mode 100644 index 00000000..f0c02a27 --- /dev/null +++ b/.agents/skills/filigree-workflow/SKILL.md @@ -0,0 +1,304 @@ +--- +name: filigree-workflow +description: > + This skill should be used when the user asks to "track work", "create an issue", + "find something to work on", "what should I work on next", "triage bugs", "close + an issue", "check what's blocked", "plan a milestone", "review sprint progress", + "coordinate agents", or when working in a project that uses filigree for issue + tracking. Provides workflow patterns, team coordination protocols, and operational + guidance for the filigree issue tracker. +--- + +# Filigree Workflow + +Filigree is an agent-native issue tracker that stores data locally in `.filigree/`. +This skill provides procedural knowledge for using filigree effectively — as a solo +agent or in a multi-agent swarm. + +## Core Workflow + +Every task follows this lifecycle: + +``` +filigree ready → find available work (no blockers) +filigree show → read requirements and context +filigree transitions → check valid status transitions +filigree start-work --assignee → atomically claim + transition to in_progress +[do the work, commit code] +filigree close --reason="summary of what was done" +``` + +Or skip steps 1–3 entirely with `filigree start-next-work --assignee ` to grab the highest-priority ready issue. + +Always close with a `--reason` — it becomes audit trail for the next agent. + +## Priority Semantics + +| Priority | Meaning | Action | +|----------|---------|--------| +| P0 | Critical | Drop everything. Production is broken. | +| P1 | High | Do next. Current sprint must-have. | +| P2 | Medium | Default. Normal backlog work. | +| P3 | Low | Nice to have. Do when P1/P2 are clear. | +| P4 | Backlog | Someday. Don't schedule unless promoted. | + +When triaging, use `filigree batch-update --priority=N` for bulk changes. + +## Starting Work + +### Solo or Swarm — Same Tool + +Use `start-work` (or `start-next-work`) for the usual case. Both atomically +claim the issue *and* transition it to `in_progress` in one DB transaction — +optimistic-locking on the assignee, so concurrent callers can't both think +they own the issue. + +```bash +filigree start-work --assignee # specific issue +filigree start-next-work --assignee # highest-priority ready +``` + +If another agent already owns the claim, the call fails with `code: CONFLICT` +(CLI exit 4). Safe to retry against a different issue. + +### Niche: Claim Without Transitioning + +`claim` and `claim-next` still exist for the rare case where you want to +reserve an issue but not advance its status (e.g. a coordinator earmarking +work for a worker that will pick it up later). Prefer `start-work` for +normal flow. + +```bash +filigree claim --assignee # reserve only, no transition +filigree claim-next --assignee +``` + +## Key Commands + +### Finding Work + +```bash +filigree ready # ready issues sorted by priority +filigree list --status=open # all open issues +filigree search "auth" # full-text search +filigree critical-path # longest dependency chain +``` + +### Creating Issues + +```bash +filigree create "Title" --type=bug --priority=1 +filigree create "Title" --type=task -d "description" --dep +filigree create-plan --file plan.json # milestone/phase/step hierarchy +``` + +### Managing Dependencies + +```bash +filigree add-dep # A depends on B +filigree remove-dep +filigree blocked # show all blocked issues +``` + +### Context and Handoff + +```bash +filigree add-comment "what I found / what's left to do" +filigree get-comments # read previous context +filigree show # full details including deps +``` + +Always add a comment before closing or handing off — the next agent has no memory +of the current conversation. + +## Workflow Patterns + +### Before Starting Work + +1. Run `filigree ready` to see available work +2. Check `filigree critical-path` — unblocking the critical path has highest leverage +3. Pick work that matches the current session's context (e.g., if code is already open) + +### When Finishing Work + +1. Add a comment summarising what was done and any follow-up needed +2. Close with a reason: `filigree close --reason="implemented X, tested Y"` +3. Check if closing this issue unblocks anything: `filigree ready` + +### When Blocked + +1. Add a comment explaining the blocker +2. Create the blocking issue if it doesn't exist +3. Add the dependency: `filigree add-dep ` +4. Move to other available work + +## Guidance Sheets + +For detailed patterns, consult these reference files: + +- **`references/workflow-patterns.md`** — Triage flows, sprint planning, + dependency management, bug lifecycle patterns +- **`references/team-coordination.md`** — Multi-agent swarm protocols, + handoff conventions, claiming strategies, status update patterns +- **`examples/sprint-plan.json`** — Complete create-plan input template + with cross-phase dependencies + +Load these when facing a specific workflow challenge rather than reading upfront. + +## File Records & Scan Findings + +The dashboard API tracks files and scan findings across the project. Use the +schema discovery endpoint to find valid values and available endpoints: + +``` +GET /api/files/_schema +``` + +This returns valid severities, finding statuses, association types, sort fields, +and a full endpoint catalog. When linking issues to files, use file associations: + +| Association Type | Meaning | +|-----------------|---------| +| `bug_in` | Bug reported in this file | +| `task_for` | Task related to this file | +| `scan_finding` | Automated scan finding | +| `mentioned_in` | File referenced in issue | + +## Response Shapes (2.0) + +When parsing `--json` output or MCP responses, expect these unified envelopes: + +- **Batch ops** → `{succeeded: [...], failed: [{id, error, code}, ...], newly_unblocked?: [...]}`. + `failed` is always present (empty list if none); `newly_unblocked` is + omitted when the op cannot unblock. Pass `--detail=full` (CLI) or + `response_detail="full"` (MCP) to get full records back. +- **List ops** → `{items: [...], has_more: bool, next_offset?: int}`. + `next_offset` only appears when there is a next page. +- **Errors** → `{error: str, code: ErrorCode, details?: dict}`. `code` is + one of: `VALIDATION`, `NOT_FOUND`, `CONFLICT`, `INVALID_TRANSITION`, + `PERMISSION`, `NOT_INITIALIZED`, `IO`, `INVALID_API_URL`, `STOP_FAILED`, + `SCHEMA_MISMATCH`, `INTERNAL`. Branch on `code` for retry policy + (`CONFLICT` → exit 4, retryable; everything at exit 1 needs operator + intervention). + +The issue ID is always `issue_id` in 2.0 — in MCP inputs, response payloads, +and CLI JSON. Status is always `status`; "state" was retired as a +user-facing word. + +## Health and Diagnostics + +```bash +filigree doctor # check installation health +filigree stats # project-wide counts +filigree metrics # cycle time, lead time, throughput +filigree events # audit trail for a specific issue +``` + +## Observations — Ambient Note-Taking + +Observations are a scratchpad for things you notice *while doing other work*. They +are not issues — they're lightweight, expiring notes that let you capture a thought +without breaking flow. + +### When to Observe + +Observations are for **incidental** defects — things you notice *in passing* +while working on something else, that fall *outside the scope of your current +task*. The core use case is: "I don't have time to investigate this right now, +but I want to come back to it." + +Examples of good observations: + +- A code smell in a neighbouring file you happened to read +- A missing test for an edge case unrelated to what you're changing +- A potential bug in a module you're not touching +- A TODO or FIXME that looks stale +- A dependency that might be outdated + +**Always include `file_path` and `line`** when the observation is about specific code. +This anchors it for whoever triages it later. + +### When NOT to Observe + +**You fix bugs in your currently defined scope. You do NOT use observations to +finish work prematurely.** + +If you're working on task X and you notice that your implementation of X has a +gap, a missed edge case, an untested branch, a known shortcoming, or a piece of +follow-up that "should really be done too" — that is **task scope, not an +observation**. You own it. Handle it one of these ways instead: + +- **Fix it now** as part of the current task. (Default.) +- **Expand the task** (or split a sub-task) and address it in this work stream. +- **File a proper issue** with a dependency on the current task, so the gap is + visible in the work record before you close. +- **Surface it to the user** if it changes the shape of what you're delivering. + +Filing your own task's deficiencies as observations and closing the task is +**not** completing the task. It is shipping known-broken work and hiding the +debt in a 14-day expiring scratchpad — where it will quietly rot, get +auto-dismissed, and never be addressed. The work record must reflect what is +actually outstanding. + +**The test:** *"Would I have noticed this even if I weren't working on this +task?"* If yes → observation. If no → it's part of the work, fix it. + +**Don't observe things that are clearly issues either.** If you're confident +something is a bug or a needed feature, create an issue directly. Observations +are for "hmm, this might be worth looking at" — the uncertain middle ground. + +### Triage Workflow + +Observations expire after 14 days. Triage them before they rot: + +1. **At session end:** run `list_observations` and quickly scan what's accumulated +2. **For each observation, decide:** + - **Dismiss** — not actionable, already fixed, or not worth tracking. Use + `dismiss_observation` with a brief reason for the audit trail. + - **Promote** — deserves to be tracked as an issue. Use `promote_observation` + which atomically creates an issue and labels it `from-observation`. Choose + the right issue type: + - `type='bug'` — something is broken or produces wrong results + - `type='task'` (default) — cleanup, improvement, or "this works but is shitty" + - `type='feature'` — a missing capability that should exist + - `type='requirement'` — a formal requirement to be reviewed, approved, and verified, when the requirements pack is enabled + - **Leave it** — still uncertain. Let it age. If it survives a few sessions + without being promoted, it's probably a dismiss. + +3. **Batch cleanup:** use the MCP tool `batch_dismiss_observations` when several observations + have gone stale together. + +### Promote vs Dismiss + +| Signal | Action | +|--------|--------| +| You noticed it twice in separate sessions | Promote | +| It's in a hot code path or critical module | Promote | +| It has a clear fix or next step | Promote | +| It was about code that's since been refactored | Dismiss | +| It's a style/taste preference, not a defect | Dismiss | +| You can't articulate what the fix would be | Leave it (or dismiss if > 7 days old) | + +### Tracking the Pipeline + +Promoted observations get the `from-observation` label. To see the pipeline output: + +```bash +filigree list --label=from-observation # All promoted observations +filigree search "from-observation" # Search with context +``` + +## Quick Decision Guide + +| Situation | Action | +|-----------|--------| +| "What should I work on?" | `filigree ready`, pick highest priority | +| "Is this blocked?" | `filigree show `, check blocked_by | +| "Multiple agents need work" | `filigree start-next-work --assignee ` | +| "I found a new bug" | `filigree create "..." --type=bug --priority=1` | +| "This task is bigger than expected" | Create sub-tasks, add deps | +| "I'm done" | Comment, close with reason, check `ready` | +| "Something changed while I worked" | `filigree changes --since ` | +| "I noticed something odd in a file I'm passing through" | `observe` with file_path and line — keep working | +| "I noticed a gap in the work I'm currently doing" | Fix it, expand the task, or file a proper issue — **do not** observe it | +| "These observations are piling up" | `list_observations`, then dismiss or promote each | diff --git a/.agents/skills/filigree-workflow/examples/sprint-plan.json b/.agents/skills/filigree-workflow/examples/sprint-plan.json new file mode 100644 index 00000000..af4bb09b --- /dev/null +++ b/.agents/skills/filigree-workflow/examples/sprint-plan.json @@ -0,0 +1,30 @@ +{ + "milestone": { + "title": "Sprint 3 — Auth & Dashboard", + "priority": 1 + }, + "phases": [ + { + "title": "Backend API", + "steps": [ + {"title": "Auth endpoint (JWT token issuance)", "priority": 1}, + {"title": "User CRUD endpoints", "priority": 2, "deps": [0]}, + {"title": "Rate limiting middleware", "priority": 2, "deps": [0]} + ] + }, + { + "title": "Frontend", + "steps": [ + {"title": "Login page", "priority": 1, "deps": ["0.0"]}, + {"title": "Dashboard layout", "priority": 2, "deps": ["0.1"]} + ] + }, + { + "title": "Integration & QA", + "steps": [ + {"title": "End-to-end auth flow test", "priority": 1, "deps": ["1.0"]}, + {"title": "Load test rate limiter", "priority": 3, "deps": ["0.2"]} + ] + } + ] +} diff --git a/.agents/skills/filigree-workflow/references/team-coordination.md b/.agents/skills/filigree-workflow/references/team-coordination.md new file mode 100644 index 00000000..9f5c24a4 --- /dev/null +++ b/.agents/skills/filigree-workflow/references/team-coordination.md @@ -0,0 +1,197 @@ +# Team Coordination + +Multi-agent swarm protocols for filigree 2.0. Load this reference when coordinating +work across multiple agents. + +## Atomic Start + +### The Race Condition Problem + +When multiple agents call `filigree update --status=in_progress` +simultaneously, both think they own the issue. Filigree 2.0 solves this with +`start-work`, which atomically claims the issue *and* transitions it to +`in_progress` in a single DB transaction with optimistic locking on the +assignee. + +### Start Protocol + +```bash +# Option A: Start a specific issue +filigree start-work --assignee + +# Option B: Start the highest-priority ready issue +filigree start-next-work --assignee +``` + +If another agent already claimed the issue, the call fails with +`code: CONFLICT` (CLI exit 4). No silent overwrite, no half-claimed state — +either both the claim and the transition land, or neither does. + +`start-next-work` accepts the same filters as `claim-next` +(`--type`, `--priority-min`, `--priority-max`, `--target-status`) so +specialised agents can scope their work. + +### Niche: Claim Without Transitioning + +If a coordinator wants to reserve an issue without advancing its status +(e.g. earmarking it for a downstream worker), use the atomic primitives: + +```bash +filigree claim --assignee +filigree claim-next --assignee +``` + +These are kept for niche use; `start-work` is the default in 2.0. + +### Releasing Claims + +If an agent cannot finish the work: + +```bash +filigree add-comment "Releasing: blocked on X, needs Y to continue" +filigree release +``` + +Always add a comment before releasing — the next agent needs context. + +## Handoff Protocol + +When passing work between agents, follow this sequence: + +### Outgoing Agent (Finishing) + +1. **Document state**: Add a comment with current progress, decisions made, + and remaining work +2. **Update status**: Leave at `in_progress` if partially done, or close if complete +3. **Flag blockers**: Create blocker issues and add dependencies if needed + +```bash +filigree add-comment "Completed: API endpoints for auth. +Remaining: frontend login page needs the /api/token response format. +Decision: used JWT not sessions — see commit abc123. +Blocker: need CORS config before frontend can call API." +``` + +### Incoming Agent (Picking Up) + +1. **Read context**: `filigree show ` and `filigree get-comments ` +2. **Check dependencies**: Look at `blocked_by` in the show output +3. **Start**: `filigree start-work --assignee ` +4. **Continue**: Build on the previous agent's work, don't restart + +## Status Update Conventions + +### When to Update Status + +| Event | Action | +|-------|--------| +| Starting work | `start-work --assignee ` (atomic claim + transition) | +| Hit a blocker | Add comment, create blocker issue, add dep | +| Completed the work | `close --reason="..."` | +| Can't finish, releasing | Comment + `release` | +| Found additional work | Create new issues, add deps if needed | + +### Comment Conventions + +Prefix comments with context markers for quick scanning: + +```bash +filigree add-comment "PROGRESS: implemented X and Y, Z remaining" +filigree add-comment "BLOCKED: waiting on for API schema" +filigree add-comment "DECISION: chose approach A because of B" +filigree add-comment "HANDOFF: releasing, next agent should start at Z" +``` + +## Swarm Work Distribution + +### Leader-Follower Pattern + +One agent acts as coordinator: + +1. **Leader** runs `filigree ready` and assigns work (or pre-claims via `claim`) +2. **Followers** use `filigree start-work --assignee ` to take it on +3. **Followers** report back via comments when done +4. **Leader** monitors `filigree stats` and `filigree list --status=in_progress` + +### Self-Organising Pattern + +All agents are peers: + +1. Each agent runs `filigree start-next-work --assignee ` +2. Works on the started issue independently +3. Closes and immediately calls `start-next-work` again +4. No central coordinator needed + +This works best when: +- Issues are well-defined and independent +- Dependencies are properly wired (so `start-next-work` only returns unblocked work) +- Priority ordering reflects actual importance + +Tie-break ordering for `start-next-work` (and `claim-next`): +1. `priority` ascending (0 = critical first) +2. `created_at` ascending (oldest first within a priority tier) +3. `issue_id` ascending (deterministic tie-break) + +### Filtering by Type + +Specialised agents can filter their start calls: + +```bash +# Backend agent +filigree start-next-work --assignee backend-1 --type task + +# Bug-fixing agent +filigree start-next-work --assignee bugfix-1 --type bug --priority-max 1 +``` + +## Conflict Resolution + +### Two Agents Modified the Same Code + +1. The second agent's commit will show merge conflicts +2. Add a comment on the issue explaining the conflict +3. The agent with the simpler change should rebase +4. Use `filigree add-comment` to document the resolution + +### Two Agents Claimed Related Work + +If agents discover their tasks overlap: + +1. One agent adds a dependency between the tasks +2. The agent with the lower-priority task releases their claim +3. The remaining agent completes the prerequisite first + +### Stale Claims + +If an agent disappears without completing work: + +```bash +filigree list --status=in_progress --assignee +filigree release # free the claim +filigree add-comment "Released: previous agent did not complete" +``` + +### CONFLICT Responses + +A `start-work` (or `claim`) call that loses the race returns +`{error: ..., code: "CONFLICT", details: {current_assignee: "..."}}` and +exits with code 4. This is distinct from operational errors (exit 1) so +automated callers can retry against a different issue without escalating. + +## Session Resumption + +When an agent starts a new session and needs to resume context: + +```bash +# What was I working on? +filigree list --status=in_progress --assignee + +# What happened since I last worked? +filigree changes --since + +# What's ready now? +filigree ready +``` + +The `filigree session-context` hook does this automatically at session start, +but these commands are useful for manual context recovery. diff --git a/.agents/skills/filigree-workflow/references/workflow-patterns.md b/.agents/skills/filigree-workflow/references/workflow-patterns.md new file mode 100644 index 00000000..14fb10ff --- /dev/null +++ b/.agents/skills/filigree-workflow/references/workflow-patterns.md @@ -0,0 +1,168 @@ +# Workflow Patterns + +Detailed procedural patterns for common filigree workflows. Load this reference +when facing a specific workflow challenge. + +## Triage Pattern + +Triage turns an unsorted pile of issues into a prioritised, actionable backlog. + +### Process + +1. **Gather**: `filigree list --status=open --json` to get all open issues +2. **Categorise by type**: Separate bugs from features from tasks +3. **Set priorities**: + - P0/P1 for anything blocking users or other work + - P2 for standard backlog items + - P3/P4 for nice-to-haves and future ideas +4. **Batch update**: `filigree batch-update --priority=N` +5. **Add dependencies**: Wire up blocking relationships so `ready` reflects reality +6. **Verify**: `filigree ready` should now show a clean, prioritised work queue + +### Anti-patterns + +- Setting everything to P1 — defeats the purpose of priorities +- Skipping dependency wiring — agents pick blocked work and waste time +- Triaging without reading descriptions — priorities should reflect actual impact + +## Sprint Planning Pattern + +Plan a focused set of work for a bounded time period. + +### Using Milestones + +```bash +# Create the plan structure +filigree create-plan --file sprint.json +``` + +See `examples/sprint-plan.json` for a complete template. The key structure: + +```json +{ + "milestone": {"title": "Sprint 3", "priority": 1}, + "phases": [ + { + "title": "Phase name", + "steps": [ + {"title": "Step A", "priority": 1}, + {"title": "Step B", "deps": [0]} + ] + } + ] +} +``` + +Dependencies use indices: integer for same-phase (`0` = first step), cross-phase +uses `"phase.step"` format (`"0.0"` = phase 0, step 0). + +### Tracking Progress + +```bash +filigree plan # tree view with progress bars +filigree stats # overall project health +filigree metrics --days 14 # velocity for this sprint period +``` + +## Dependency Management + +### When to Add Dependencies + +- Task B cannot start until task A's output exists (data dependency) +- Task B would be invalidated by task A's changes (ordering dependency) +- Task B is a sub-task of epic A (parent-child, not a dep — use `--parent`) + +### When NOT to Add Dependencies + +- Tasks are merely related but can proceed independently +- The ordering is preferred but not required +- One task "should" be done first but the other won't break without it + +### Debugging Blocked Work + +```bash +filigree blocked # all blocked issues with blockers +filigree critical-path # longest chain to unblock +filigree show # see what blocks this specific issue +``` + +To unblock: close the blocker, or if the dependency is wrong, remove it: +```bash +filigree remove-dep +``` + +## Bug Lifecycle + +### Standard Flow + +``` +create (open) → in_progress → closed +``` + +Use `filigree start-work --assignee ` to make the +`open → in_progress` transition atomically. + +### With Verification + +For types that support it (check `filigree type-info bug`): + +``` +open → fixing → verifying → closed +``` + +Pass `--target-status fixing` to `start-work` if the workflow has multiple +`wip`-category targets and the resolver needs disambiguation. + +### Bug Report Template + +```bash +filigree create "Short description" \ + --type=bug \ + --priority=1 \ + -d "Steps to reproduce: ... +Expected: ... +Actual: ... +Impact: ..." +``` + +### After Fixing + +Always add a comment with: +1. Root cause explanation +2. What was changed +3. How it was tested + +```bash +filigree add-comment "Root cause: off-by-one in pagination. +Fixed in commit abc123. Tested with 0, 1, and boundary cases." +filigree close --reason="Fixed off-by-one in pagination logic" +``` + +## Event History and Auditing + +### Reviewing What Happened + +```bash +filigree events # full history for one issue +filigree changes --since 2026-01-15T00:00:00 # everything since a timestamp +``` + +### Undoing Mistakes + +```bash +filigree undo # reverts last reversible action (status, priority, etc.) +``` + +Only reversible actions can be undone. Check `filigree events ` first to +see what the last action was. + +## Archiving and Maintenance + +### Cleaning Up Old Issues + +```bash +filigree archive --days 30 # archive issues closed >30 days ago +filigree compact --keep 50 # trim event history for archived issues +``` + +Archive when the active issue count exceeds ~500 and queries start slowing down. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 466134dc..e4cd32b3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,6 +29,11 @@ jobs: - name: fmt run: cargo fmt --all -- --check + - name: migration retirement guard + run: | + python scripts/check-migration-retirement.py --self-test + python scripts/check-migration-retirement.py + - name: clippy run: cargo clippy --workspace --all-targets --all-features -- -D warnings @@ -75,6 +80,11 @@ jobs: - name: check B.4* gate result freshness run: python scripts/check-b4-gate-result.py + - name: check Python ontology version lockstep + run: | + python scripts/check-python-ontology-version.py --self-test + python scripts/check-python-ontology-version.py + - name: install plugin (dev extras) run: python -m pip install -e 'plugins/python[dev]' diff --git a/.gitignore b/.gitignore index 5976e682..17baed25 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,5 @@ __pycache__/ .coverage htmlcov/ .claude/ + +.env \ No newline at end of file diff --git a/.mcp.json b/.mcp.json index 91d793bb..24a20674 100644 --- a/.mcp.json +++ b/.mcp.json @@ -5,6 +5,16 @@ "command": "/home/john/.local/bin/filigree-mcp", "args": [], "env": {} + }, + "clarion": { + "type": "stdio", + "command": "/home/john/clarion/target/release/clarion", + "args": [ + "serve", + "--path", "/tmp/clarion-b8-elspeth-full-20260518T0016Z", + "--config", "/tmp/clarion-b8-elspeth-full-20260518T0016Z/clarion-b8-live.yaml" + ], + "env": {} } } } \ No newline at end of file diff --git a/CLAUDE.md b/CLAUDE.md index d15aa5b7..edec3c26 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -138,3 +138,106 @@ These were filed during Sprint 1 with explicit deferral rationale and are ready - `clarion-889200006a` (P3, sprint:2 / wp:9) — ADR-018 amendment: L7 qualname divergence with Wardline `FingerprintEntry`. Triggers when WP9 attempts the first cross-product join. - WP2 deferred items: `clarion-48c5d06578` (supervisor drain/discard), `clarion-928349b60f` (jail TOCTOU on briefing read), `clarion-35688034f0` (read_frame deadline), `clarion-c0977ac293` (RLIMIT_AS observed end-to-end), `clarion-adeff0916d` (fixture-binary self-build). - WP1 review-2 P2 bugs: `clarion-5e03cfdd21`, `clarion-ed5017139f`, `clarion-b5b1029f5a`, `clarion-4cd11905e2` — good Sprint-2 warm-up before Tier-B feature work. + + +## Filigree Issue Tracker + +`filigree` tracks tasks for this project. Data lives in `.filigree/`. Prefer +the MCP tools (`mcp__filigree__*`) when available; fall back to the `filigree` +CLI otherwise. + +### Workflow + +```bash +# At session start +filigree session-context # ready / in-progress / critical path + +# Pick up the next ready issue (atomic claim + transition to in_progress) +filigree start-next-work --assignee +# ...or claim a specific issue +filigree start-work --assignee + +# Do the work, commit, then +filigree close +``` + +Use the atomic claim+transition verbs — `start_work` / `start_next_work` +(MCP) or `start-work` / `start-next-work` (CLI). Do **not** chain +`claim_issue` (MCP) or `filigree claim` (CLI) with a subsequent status +update — the two-step form races against other agents; the combined verb is +atomic. + +### Observations: when (and when not) to use them + +`observe` is a fire-and-forget scratchpad for *incidental* defects — things +you notice *outside the scope of your current task* (a code smell in a +neighbouring file, a stale TODO, a missing test for an edge case you happened +to spot). Notes expire after 14 days unless promoted. Include `file_path` and +`line` when relevant. At session end, skim `list_observations` and either +`dismiss_observation` or `promote_observation` for what has accumulated. + +**You fix bugs in your currently defined scope. You do NOT use observations +to finish work prematurely.** If a defect, gap, or follow-up belongs to your +current task, you own it — handle it as part of that task: fix it now, expand +the task's scope, file a proper issue with a dependency, or surface it to the +user. Filing it as an observation and closing the task is *not* completing +the task; it is shipping known-broken work and hiding the debt in a 14-day +expiring scratchpad. The test is "would I have noticed this even if I weren't +working on this task?" If no, it's task scope, not an observation. + +### Priority scale + +- P0: Critical (drop everything) +- P1: High (do next) +- P2: Medium (default) +- P3: Low +- P4: Backlog + +### Reaching for tools + +MCP tool schemas describe each tool; `filigree --help` and `filigree +--help` are the authoritative CLI reference. You do not need to memorise +either catalogue. The verbs you will reach for most: + +- **Find work:** `get_ready`, `get_blocked`, `list_issues`, `search_issues` +- **Claim work:** `start_work`, `start_next_work` +- **Update:** `add_comment`, `add_label`, `update_issue`, `close_issue` +- **Scratchpad:** `observe`, `list_observations`, `promote_observation`, `dismiss_observation` +- **Cross-product entity bindings (ADR-029):** `add_entity_association`, + `remove_entity_association`, `list_entity_associations`, + `list_associations_by_entity`. Used when a sibling tool (e.g. + Clarion) needs to bind a Filigree issue to a function, class, or + module identifier it owns. The `entity_id` is an opaque string + from Filigree's perspective; the consumer (the sibling tool's read + path) does drift detection against the stored + `content_hash_at_attach`. `list_associations_by_entity` is the + reverse-lookup surface — given a Clarion entity ID, return every + Filigree issue bound to it (project isolation is by DB file). Also + reachable over HTTP as + `GET/POST /api/issue/{issue_id}/entity-associations`, + `DELETE /api/issue/{issue_id}/entity-associations?entity_id=…`, + and `GET /api/entity-associations?entity_id=…`. +- **Health:** `get_stats`, `get_metrics`, `get_mcp_status` + +Pass `--actor ` (CLI) so events attribute to your agent identity. + +### Error handling + +Errors return `{error: str, code: ErrorCode, details?: dict}`. Switch on +`code`, not on message text. Codes: `VALIDATION`, `NOT_FOUND`, `CONFLICT`, +`INVALID_TRANSITION`, `PERMISSION`, `NOT_INITIALIZED`, `IO`, +`INVALID_API_URL`, `STOP_FAILED`, `SCHEMA_MISMATCH`, `INTERNAL`. + +On `INVALID_TRANSITION`, call `get_valid_transitions` (MCP) or +`filigree transitions ` to see what the workflow allows from here. + +Two failure modes deserve a specific response: + +- **`SCHEMA_MISMATCH`** — the installed `filigree` is older than the project + database. The error message contains upgrade guidance. Surface it to the + user; do not retry. +- **`ForeignDatabaseError`** — filigree found a parent project's database + but no local `.filigree.conf`. Run `filigree init` in the current + directory. Do **not** `cd` upward to a different project unless that was + the actual intent. + diff --git a/Cargo.lock b/Cargo.lock index 802e190e..2a433f0e 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -112,6 +112,12 @@ version = "1.1.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1505bd5d3d116872e7271a6d4e16d81d0c8570876c8de68093a09ac269d8aac0" +[[package]] +name = "autocfg" +version = "1.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8" + [[package]] name = "base64" version = "0.22.1" @@ -135,7 +141,16 @@ dependencies = [ "cc", "cfg-if", "constant_time_eq", - "cpufeatures", + "cpufeatures 0.3.0", +] + +[[package]] +name = "block-buffer" +version = "0.10.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71" +dependencies = [ + "generic-array", ] [[package]] @@ -241,13 +256,20 @@ dependencies = [ "clarion-mcp", "clarion-plugin-fixture", "clarion-storage", + "dotenvy", + "ignore", "rusqlite", + "serde", "serde_json", + "serde_norway", + "sha2", "tempfile", + "time", "tokio", "tracing", "tracing-subscriber", "uuid", + "xgraph", ] [[package]] @@ -268,6 +290,7 @@ dependencies = [ name = "clarion-mcp" version = "0.1.0-dev" dependencies = [ + "blake3", "clarion-core", "clarion-storage", "reqwest", @@ -277,6 +300,7 @@ dependencies = [ "serde_norway", "tempfile", "thiserror 1.0.69", + "time", "tokio", ] @@ -285,6 +309,7 @@ name = "clarion-plugin-fixture" version = "0.1.0-dev" dependencies = [ "clarion-core", + "nix", "serde_json", ] @@ -330,6 +355,15 @@ version = "0.8.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "773648b94d0e5d620f64f280777445740e61fe701025087ec8b57f45c791888b" +[[package]] +name = "cpufeatures" +version = "0.2.17" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "59ed5838eebb26a2bb2e58f6d5b5316989ae9d08bab10e0e6d103e656d1b0280" +dependencies = [ + "libc", +] + [[package]] name = "cpufeatures" version = "0.3.0" @@ -339,6 +373,41 @@ dependencies = [ "libc", ] +[[package]] +name = "crossbeam-deque" +version = "0.8.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9dd111b7b7f7d55b72c0a6ae361660ee5853c9af73f70c3c2ef6858b950e2e51" +dependencies = [ + "crossbeam-epoch", + "crossbeam-utils", +] + +[[package]] +name = "crossbeam-epoch" +version = "0.9.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e" +dependencies = [ + "crossbeam-utils", +] + +[[package]] +name = "crossbeam-utils" +version = "0.8.21" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d0a5c400df2834b80a4c3327b3aad3a4c4cd4de0629063962b03235697506a28" + +[[package]] +name = "crypto-common" +version = "0.1.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "78c8292055d1c1df0cce5d180393dc8cce0abec0a7102adb6c7b1eef6016d60a" +dependencies = [ + "generic-array", + "typenum", +] + [[package]] name = "deadpool" version = "0.12.3" @@ -380,12 +449,31 @@ dependencies = [ "deadpool-runtime", ] +[[package]] +name = "deranged" +version = "0.5.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7cd812cc2bc1d69d4764bd80df88b4317eaef9e773c75226407d9bc0876b211c" +dependencies = [ + "powerfmt", +] + [[package]] name = "difflib" version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "6184e33543162437515c2e2b48714794e37845ec9851711914eec9d308f6ebe8" +[[package]] +name = "digest" +version = "0.10.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292" +dependencies = [ + "block-buffer", + "crypto-common", +] + [[package]] name = "displaydoc" version = "0.2.5" @@ -397,6 +485,12 @@ dependencies = [ "syn", ] +[[package]] +name = "dotenvy" +version = "0.15.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1aaf95b3e5c8f23aa320147307562d361db0ae0d51242340f558153b4eb2439b" + [[package]] name = "equivalent" version = "1.0.2" @@ -437,6 +531,15 @@ version = "0.1.9" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5baebc0774151f905a1a2cc41989300b1e6fbb29aff0ceffa1064fdd3088d582" +[[package]] +name = "float-cmp" +version = "0.10.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b09cf3155332e944990140d967ff5eceb70df778b34f77d8075db46e4704e6d8" +dependencies = [ + "num-traits", +] + [[package]] name = "foldhash" version = "0.1.5" @@ -501,6 +604,16 @@ dependencies = [ "slab", ] +[[package]] +name = "generic-array" +version = "0.14.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a" +dependencies = [ + "typenum", + "version_check", +] + [[package]] name = "getrandom" version = "0.2.17" @@ -541,6 +654,19 @@ dependencies = [ "wasip3", ] +[[package]] +name = "globset" +version = "0.4.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "52dfc19153a48bde0cbd630453615c8151bce3a5adfac7a0aebfbf0a1e1f57e3" +dependencies = [ + "aho-corasick", + "bstr", + "log", + "regex-automata", + "regex-syntax", +] + [[package]] name = "hashbrown" version = "0.14.5" @@ -792,6 +918,22 @@ dependencies = [ "icu_properties", ] +[[package]] +name = "ignore" +version = "0.4.25" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d3d782a365a015e0f5c04902246139249abf769125006fbe7649e2ee88169b4a" +dependencies = [ + "crossbeam-deque", + "globset", + "log", + "memchr", + "regex-automata", + "same-file", + "walkdir", + "winapi-util", +] + [[package]] name = "indexmap" version = "2.14.0" @@ -934,6 +1076,21 @@ dependencies = [ "windows-sys 0.61.2", ] +[[package]] +name = "num-conv" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c6673768db2d862beb9b39a78fdcb1a69439615d5794a1be50caa9bc92c81967" + +[[package]] +name = "num-traits" +version = "0.2.19" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841" +dependencies = [ + "autocfg", +] + [[package]] name = "num_cpus" version = "1.17.0" @@ -989,6 +1146,12 @@ dependencies = [ "zerovec", ] +[[package]] +name = "powerfmt" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391" + [[package]] name = "ppv-lite86" version = "0.2.21" @@ -1312,6 +1475,15 @@ version = "1.0.23" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9774ba4a74de5f7b1c1451ed6cd5285a32eddb5cccb8cc655a4e50009e06477f" +[[package]] +name = "same-file" +version = "1.0.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502" +dependencies = [ + "winapi-util", +] + [[package]] name = "schannel" version = "0.1.29" @@ -1427,6 +1599,17 @@ dependencies = [ "serde", ] +[[package]] +name = "sha2" +version = "0.10.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a7507d819769d01a365ab707794a4084392c824f54a7a6a7862f8c3d0892b283" +dependencies = [ + "cfg-if", + "cpufeatures 0.2.17", + "digest", +] + [[package]] name = "sharded-slab" version = "0.1.7" @@ -1581,6 +1764,37 @@ dependencies = [ "cfg-if", ] +[[package]] +name = "time" +version = "0.3.47" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "743bd48c283afc0388f9b8827b976905fb217ad9e647fae3a379a9283c4def2c" +dependencies = [ + "deranged", + "itoa", + "num-conv", + "powerfmt", + "serde_core", + "time-core", + "time-macros", +] + +[[package]] +name = "time-core" +version = "0.1.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7694e1cfe791f8d31026952abf09c69ca6f6fa4e1a1229e18988f06a04a12dca" + +[[package]] +name = "time-macros" +version = "0.2.27" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2e70e4c5a0e0a8a4823ad65dfe1a6930e4f4d756dcd9dd7939022b5e8c501215" +dependencies = [ + "num-conv", + "time-core", +] + [[package]] name = "tinystr" version = "0.8.3" @@ -1795,6 +2009,12 @@ version = "0.2.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e421abadd41a4225275504ea4d6566923418b7f05506fbc9c0fe86ba7396114b" +[[package]] +name = "typenum" +version = "1.20.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "40ce102ab67701b8526c123c1bab5cbe42d7040ccfd0f64af1a385808d2f43de" + [[package]] name = "unicode-ident" version = "1.0.24" @@ -1881,6 +2101,16 @@ dependencies = [ "libc", ] +[[package]] +name = "walkdir" +version = "2.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b" +dependencies = [ + "same-file", + "winapi-util", +] + [[package]] name = "want" version = "0.3.1" @@ -2023,6 +2253,15 @@ dependencies = [ "wasm-bindgen", ] +[[package]] +name = "winapi-util" +version = "0.1.11" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22" +dependencies = [ + "windows-sys 0.61.2", +] + [[package]] name = "windows-link" version = "0.2.1" @@ -2294,6 +2533,17 @@ version = "0.6.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1ffae5123b2d3fc086436f8834ae3ab053a283cfac8fe0a0b8eaae044768a4c4" +[[package]] +name = "xgraph" +version = "2.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3486b48dbc3ca08eca1144243e8f7d942b7cb7b6c0383ea00b9492665d862752" +dependencies = [ + "float-cmp", + "rand", + "slab", +] + [[package]] name = "yoke" version = "0.8.2" diff --git a/Cargo.toml b/Cargo.toml index d6b1e9e6..4e6faf8e 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -13,7 +13,7 @@ version = "0.1.0-dev" edition = "2024" license = "MIT OR Apache-2.0" repository = "https://github.com/qacona/clarion" -rust-version = "1.85" +rust-version = "1.88" [workspace.lints.rust] # Changed from "forbid" to "deny" to allow the single documented unsafe use: @@ -34,17 +34,22 @@ anyhow = "1" blake3 = "1.8.5" clap = { version = "4", features = ["derive"] } deadpool-sqlite = { version = "0.8", features = ["rt_tokio_1"] } +dotenvy = "0.15" +ignore = "0.4" rusqlite = { version = "0.31", features = ["bundled"] } reqwest = { version = "0.12", default-features = false, features = ["blocking", "json", "rustls-tls-native-roots"] } serde = { version = "1", features = ["derive"] } serde_json = "1" serde_norway = "0.9.42" +sha2 = "0.10" thiserror = "1" +time = { version = "0.3", features = ["formatting", "macros", "parsing"] } tokio = { version = "1", features = ["rt-multi-thread", "macros", "sync", "time"] } tracing = "0.1" tracing-subscriber = { version = "0.3", features = ["env-filter"] } uuid = { version = "1", features = ["v4"] } toml = "0.8" +xgraph = "2.0.0" assert_cmd = "2" tempfile = "3" nix = { version = "0.28", default-features = false, features = ["resource"] } diff --git a/crates/clarion-cli/Cargo.toml b/crates/clarion-cli/Cargo.toml index 9f5a86fb..2bd97d1c 100644 --- a/crates/clarion-cli/Cargo.toml +++ b/crates/clarion-cli/Cargo.toml @@ -20,12 +20,19 @@ clap.workspace = true clarion-core = { path = "../clarion-core", version = "0.1.0-dev" } clarion-mcp = { path = "../clarion-mcp", version = "0.1.0-dev" } clarion-storage = { path = "../clarion-storage", version = "0.1.0-dev" } +dotenvy.workspace = true +ignore.workspace = true rusqlite.workspace = true +serde.workspace = true serde_json.workspace = true +serde_norway.workspace = true +sha2.workspace = true +time.workspace = true tokio.workspace = true tracing.workspace = true tracing-subscriber.workspace = true uuid.workspace = true +xgraph.workspace = true [dev-dependencies] assert_cmd.workspace = true diff --git a/crates/clarion-cli/src/analyze.rs b/crates/clarion-cli/src/analyze.rs index f7e23e3b..21d44329 100644 --- a/crates/clarion-cli/src/analyze.rs +++ b/crates/clarion-cli/src/analyze.rs @@ -10,10 +10,13 @@ //! - Zero successful plugins discovered → `SkippedNoPlugins` (existing path). use std::collections::{BTreeMap, BTreeSet}; +use std::fs; use std::path::{Path, PathBuf}; -use std::{fs, io}; use anyhow::{Context, Result, bail}; +use ignore::{DirEntry, WalkBuilder}; +use rusqlite::Connection; +use time::{OffsetDateTime, macros::format_description}; use uuid::Uuid; use clarion_core::{ @@ -23,21 +26,42 @@ use clarion_core::{ }; use clarion_storage::{ DEFAULT_BATCH_SIZE, DEFAULT_CHANNEL_CAPACITY, UnresolvedCallSiteRecord, Writer, - commands::{EdgeRecord, EntityRecord, RunStatus, WriterCmd}, + commands::{EdgeRecord, EntityRecord, FindingRecord, RunStatus, WriterCmd}, + module_dependency_edges, }; +use crate::clustering::{ClusterConfig, ModuleEdge, ModuleGraph, cluster_hash, cluster_modules}; +use crate::config::{AnalyzeConfig, ClusteringConfig}; use crate::stats::P95Accumulator; +const WEAK_MODULARITY_RULE_ID: &str = "CLA-FACT-CLUSTERING-WEAK-MODULARITY"; + // ── Public entry point ──────────────────────────────────────────────────────── +#[derive(Debug, Clone, Default)] +pub(crate) struct AnalyzeOptions { + pub(crate) config_path: Option, +} + /// Run the analyze command against `project_path`. /// /// # Errors /// /// Returns an error if the target directory does not exist, has no `.clarion/` /// directory, or if the writer actor fails to start or process commands. -#[allow(clippy::too_many_lines)] pub async fn run(project_path: PathBuf) -> Result<()> { + run_with_options(project_path, AnalyzeOptions::default()).await +} + +/// Run the analyze command against `project_path` with resolved CLI options. +/// +/// # Errors +/// +/// Returns an error if the target directory does not exist, has no `.clarion/` +/// directory, if analyze config is invalid, or if the writer actor fails to +/// start or process commands. +#[allow(clippy::too_many_lines)] +pub(crate) async fn run_with_options(project_path: PathBuf, options: AnalyzeOptions) -> Result<()> { if !project_path.exists() { bail!( "target directory does not exist: {}. Pass a valid path or cd to it first.", @@ -55,18 +79,24 @@ pub async fn run(project_path: PathBuf) -> Result<()> { ); } let db_path = clarion_dir.join("clarion.db"); + let analyze_config = AnalyzeConfig::load(&project_root, options.config_path.as_deref())?; + let analyze_config_json = analyze_config.to_json_string()?; // ── Writer actor ────────────────────────────────────────────────────────── - let (writer, handle) = Writer::spawn(db_path, DEFAULT_BATCH_SIZE, DEFAULT_CHANNEL_CAPACITY) - .map_err(|e| anyhow::anyhow!("{e}")) - .context("spawn writer actor")?; + let (writer, handle) = Writer::spawn( + db_path.clone(), + DEFAULT_BATCH_SIZE, + DEFAULT_CHANNEL_CAPACITY, + ) + .map_err(|e| anyhow::anyhow!("{e}")) + .context("spawn writer actor")?; let run_id = Uuid::new_v4().to_string(); let started_at = iso8601_now(); writer .send_wait(|ack| WriterCmd::BeginRun { run_id: run_id.clone(), - config_json: "{}".into(), + config_json: analyze_config_json.clone(), started_at: started_at.clone(), ack, }) @@ -150,8 +180,11 @@ pub async fn run(project_path: PathBuf) -> Result<()> { "references_resolved_total": 0, "references_skipped_external_total": 0, "references_skipped_cap_total": 0, + "imports_skipped_external_total": 0, "unresolved_reference_sites_total": 0, "pyright_query_latency_p95_ms": 0, + "pyright_index_parse_latency_p95_ms": 0, + "extractor_parse_latency_p95_ms": 0, }) .to_string(), ack, @@ -179,8 +212,7 @@ pub async fn run(project_path: PathBuf) -> Result<()> { } // ── Walk the source tree (once, union of all extensions) ───────────────── - let source_files = collect_source_files(&project_root, &wanted_extensions) - .with_context(|| format!("walking source tree at {}", project_root.display()))?; + let source_files = collect_source_files(&project_root, &wanted_extensions); tracing::info!(file_count = source_files.len(), "source tree walk complete"); // ── Per-plugin processing ───────────────────────────────────────────────── @@ -202,8 +234,11 @@ pub async fn run(project_path: PathBuf) -> Result<()> { let mut references_resolved_total: u64 = 0; let mut references_skipped_external_total: u64 = 0; let mut references_skipped_cap_total: u64 = 0; + let mut imports_skipped_external_total: u64 = 0; let mut unresolved_reference_sites_total: u64 = 0; let mut pyright_latency = P95Accumulator::default(); + let mut pyright_index_parse_latency = P95Accumulator::default(); + let mut extractor_parse_latency = P95Accumulator::default(); let mut run_outcome: RunOutcome = RunOutcome::Completed; let mut breaker = CrashLoopBreaker::default(); let mut crash_reasons: Vec = Vec::new(); @@ -256,7 +291,7 @@ pub async fn run(project_path: PathBuf) -> Result<()> { // permanently. Treat the panic as a crash reason: it flows into the // existing crash-recording path below, ticks the crash-loop breaker, // and resolves the run via SoftFailed → CommitRun(Failed) with exit 1. - let spawn_result: Result = handle_plugin_task_join_result( + let spawn_result: Result = handle_plugin_task_join_result( tokio::task::spawn_blocking(move || { run_plugin_blocking( manifest, @@ -271,13 +306,14 @@ pub async fn run(project_path: PathBuf) -> Result<()> { ); match spawn_result { - Err(reason) => { + Err(plugin_error) => { + log_plugin_findings(&plugin_id, &plugin_error.findings); tracing::warn!( plugin_id = %plugin_id, - reason = %reason, + reason = %plugin_error.reason, "plugin crashed; recording crash and continuing to next plugin", ); - crash_reasons.push(format!("{plugin_id}: {reason}")); + crash_reasons.push(format!("{plugin_id}: {}", plugin_error.reason)); let state = breaker.record_crash(); if state == CrashLoopState::Tripped { tracing::warn!( @@ -302,29 +338,17 @@ pub async fn run(project_path: PathBuf) -> Result<()> { references_resolved_total += stats.references_resolved_total; references_skipped_external_total += stats.references_skipped_external_total; references_skipped_cap_total += stats.references_skipped_cap_total; + imports_skipped_external_total += stats.imports_skipped_external_total; unresolved_reference_sites_total += stats.unresolved_reference_sites_total; pyright_latency.record_many(stats.pyright_query_latency_ms); + pyright_index_parse_latency.record_many(stats.pyright_index_parse_latency_ms); + extractor_parse_latency.record_many(stats.extractor_parse_latency_ms); // Log findings individually (Tier B persistence is future // work). Logging only the count leaves operators guessing // whether the plugin tripped an ontology check, emitted // malformed JSON, or hit a path-jail violation. - if !findings.is_empty() { - tracing::warn!( - plugin_id = %plugin_id, - finding_count = findings.len(), - "plugin host collected findings" - ); - for f in &findings { - tracing::warn!( - plugin_id = %plugin_id, - subcode = %f.subcode, - message = %f.message, - metadata = ?f.metadata, - "plugin host finding", - ); - } - } + log_plugin_findings(&plugin_id, &findings); // Persist entities + edges via writer-actor (async side). // @@ -428,6 +452,28 @@ pub async fn run(project_path: PathBuf) -> Result<()> { }; } + let phase3_output = if matches!(run_outcome, RunOutcome::HardFailed { .. }) { + Phase3Output::not_run() + } else { + match run_phase3_clustering(&writer, &db_path, &run_id, &analyze_config).await { + Ok(output) => { + total_entity_count += output.subsystems_inserted; + total_edge_count += output.in_subsystem_edges_inserted; + if output.weak_modularity_finding { + tracing::info!(run_id = %run_id, "phase3 emitted weak-modularity finding"); + } + output + } + Err(e) => { + tracing::error!(run_id = %run_id, error = %e, "phase3 clustering failed"); + run_outcome = RunOutcome::HardFailed { + reason: format!("phase3 clustering failed: {e:#}"), + }; + Phase3Output::not_run() + } + } + }; + let completed_at = iso8601_now(); // Snapshot the writer's process-lifetime dropped-edges counter so the // run's durable stats record the dedupe count (B.3 §6). Read BEFORE @@ -439,6 +485,8 @@ pub async fn run(project_path: PathBuf) -> Result<()> { .ambiguous_edges_total .load(std::sync::atomic::Ordering::Relaxed) as u64; let pyright_query_latency_p95_ms = pyright_latency.p95_ms(); + let pyright_index_parse_latency_p95_ms = pyright_index_parse_latency.p95_ms(); + let extractor_parse_latency_p95_ms = extractor_parse_latency.p95_ms(); // Extract the failure reason (if any) before the match consumes run_outcome. let fail_reason: Option = match &run_outcome { RunOutcome::SoftFailed { reason } | RunOutcome::HardFailed { reason } => { @@ -459,8 +507,12 @@ pub async fn run(project_path: PathBuf) -> Result<()> { "references_resolved_total": references_resolved_total, "references_skipped_external_total": references_skipped_external_total, "references_skipped_cap_total": references_skipped_cap_total, + "imports_skipped_external_total": imports_skipped_external_total, "unresolved_reference_sites_total": unresolved_reference_sites_total, "pyright_query_latency_p95_ms": pyright_query_latency_p95_ms, + "pyright_index_parse_latency_p95_ms": pyright_index_parse_latency_p95_ms, + "extractor_parse_latency_p95_ms": extractor_parse_latency_p95_ms, + "clustering": phase3_output.clustering_stats.clone(), }) .to_string(); writer @@ -490,8 +542,12 @@ pub async fn run(project_path: PathBuf) -> Result<()> { "references_resolved_total": references_resolved_total, "references_skipped_external_total": references_skipped_external_total, "references_skipped_cap_total": references_skipped_cap_total, + "imports_skipped_external_total": imports_skipped_external_total, "unresolved_reference_sites_total": unresolved_reference_sites_total, "pyright_query_latency_p95_ms": pyright_query_latency_p95_ms, + "pyright_index_parse_latency_p95_ms": pyright_index_parse_latency_p95_ms, + "extractor_parse_latency_p95_ms": extractor_parse_latency_p95_ms, + "clustering": phase3_output.clustering_stats.clone(), "failure_reason": reason, }) .to_string(); @@ -541,6 +597,425 @@ pub async fn run(project_path: PathBuf) -> Result<()> { Ok(()) } +// ── Phase 3 subsystem materialisation ───────────────────────────────────────── + +#[derive(Debug, Clone)] +struct Phase3Output { + subsystems_inserted: u64, + in_subsystem_edges_inserted: u64, + weak_modularity_finding: bool, + clustering_stats: serde_json::Value, +} + +impl Phase3Output { + fn not_run() -> Self { + Self { + subsystems_inserted: 0, + in_subsystem_edges_inserted: 0, + weak_modularity_finding: false, + clustering_stats: serde_json::Value::Null, + } + } +} + +#[derive(Debug, Clone)] +struct InsertedSubsystem { + id: String, + member_count: usize, +} + +#[allow(clippy::too_many_lines)] +async fn run_phase3_clustering( + writer: &Writer, + db_path: &Path, + run_id: &str, + analyze_config: &AnalyzeConfig, +) -> Result { + let started = std::time::Instant::now(); + let config = &analyze_config.analysis.clustering; + if !config.enabled { + return Ok(Phase3Output { + subsystems_inserted: 0, + in_subsystem_edges_inserted: 0, + weak_modularity_finding: false, + clustering_stats: phase3_stats_json( + config, + config.algorithm, + "disabled", + Some("disabled"), + 0, + 0, + 0, + None, + 0, + 0, + false, + started, + ), + }); + } + + writer + .send_wait(|ack| WriterCmd::FlushRunBatch { ack }) + .await + .map_err(|e| anyhow::anyhow!("{e}")) + .context("FlushRunBatch before phase3 clustering")?; + + let conn = Connection::open(db_path).context("open read connection for phase3 clustering")?; + let module_ids = module_entity_ids(&conn).context("load module entities for phase3")?; + let edge_type_names = config + .edge_types + .iter() + .map(|edge_type| edge_type.as_str()) + .collect::>(); + let dependency_edges = module_dependency_edges(&conn, &edge_type_names) + .map_err(|e| anyhow::anyhow!("{e}")) + .context("load module dependency edges for phase3")?; + + if dependency_edges.is_empty() { + return Ok(Phase3Output { + subsystems_inserted: 0, + in_subsystem_edges_inserted: 0, + weak_modularity_finding: false, + clustering_stats: phase3_stats_json( + config, + config.algorithm, + "skipped", + Some("no_module_dependency_edges"), + module_ids.len(), + 0, + 0, + None, + 0, + 0, + false, + started, + ), + }); + } + + let graph = ModuleGraph { + modules: module_ids, + edges: dependency_edges + .iter() + .map(|edge| ModuleEdge { + from: edge.from_module_id.clone(), + to: edge.to_module_id.clone(), + reference_count: edge.reference_count, + }) + .collect(), + }; + let cluster_config = ClusterConfig { + algorithm: config.algorithm, + seed: config.seed, + resolution: config.resolution, + max_iterations: config.max_iterations, + min_cluster_size: config.min_cluster_size, + }; + let cluster_result = cluster_modules(&graph, &cluster_config).context("cluster modules")?; + + if cluster_result.communities.is_empty() { + return Ok(Phase3Output { + subsystems_inserted: 0, + in_subsystem_edges_inserted: 0, + weak_modularity_finding: false, + clustering_stats: phase3_stats_json( + config, + cluster_result.algorithm_used, + "skipped", + Some("no_clusters_emitted"), + graph.modules.len(), + graph.edges.len(), + 0, + Some(cluster_result.modularity_score), + 0, + 0, + false, + started, + ), + }); + } + + let mut inserted_subsystems = Vec::new(); + let mut in_subsystem_edges_inserted = 0_u64; + let edge_type_values = config + .edge_types + .iter() + .map(|edge_type| edge_type.as_str()) + .collect::>(); + for community in &cluster_result.communities { + let hash = cluster_hash(community); + let subsystem_id = subsystem_entity_id(&hash) + .with_context(|| format!("assemble subsystem entity id for hash {hash}"))?; + let (subsystem_name, subsystem_short_name) = subsystem_display_name(community, &hash); + let now = iso8601_now(); + let properties_json = serde_json::json!({ + "algorithm": cluster_result.algorithm_used.as_str(), + "seed": config.seed, + "resolution": config.resolution, + "max_iterations": config.max_iterations, + "modularity_score": cluster_result.modularity_score, + "cluster_hash": hash, + "member_module_ids": community, + "member_count": community.len(), + "edge_types": edge_type_values, + "weight_by": config.weight_by.as_str(), + }) + .to_string(); + writer + .send_wait(|ack| WriterCmd::InsertEntity { + entity: Box::new(EntityRecord { + id: subsystem_id.clone(), + plugin_id: "core".to_owned(), + kind: "subsystem".to_owned(), + name: subsystem_name, + short_name: subsystem_short_name, + parent_id: None, + source_file_id: None, + source_file_path: None, + source_byte_start: None, + source_byte_end: None, + source_line_start: None, + source_line_end: None, + properties_json, + content_hash: None, + summary_json: None, + wardline_json: None, + first_seen_commit: None, + last_seen_commit: None, + created_at: now.clone(), + updated_at: now, + }), + ack, + }) + .await + .map_err(|e| anyhow::anyhow!("{e}")) + .with_context(|| format!("InsertEntity subsystem {subsystem_id}"))?; + + for module_id in community { + writer + .send_wait(|ack| WriterCmd::InsertEdge { + edge: Box::new(EdgeRecord { + kind: "in_subsystem".to_owned(), + from_id: module_id.clone(), + to_id: subsystem_id.clone(), + confidence: clarion_core::EdgeConfidence::Resolved, + properties_json: None, + source_file_id: None, + source_byte_start: None, + source_byte_end: None, + }), + ack, + }) + .await + .map_err(|e| anyhow::anyhow!("{e}")) + .with_context(|| { + format!("InsertEdge in_subsystem {module_id} -> {subsystem_id}") + })?; + in_subsystem_edges_inserted += 1; + } + + inserted_subsystems.push(InsertedSubsystem { + id: subsystem_id, + member_count: community.len(), + }); + } + + let weak_modularity_finding_emitted = if config.weak_modularity_threshold > 0.0 + && cluster_result.modularity_score < config.weak_modularity_threshold + { + insert_weak_modularity_finding( + writer, + run_id, + config, + &inserted_subsystems, + cluster_result.modularity_score, + ) + .await? + } else { + false + }; + + let subsystems_inserted = u64::try_from(inserted_subsystems.len()).unwrap_or(u64::MAX); + Ok(Phase3Output { + subsystems_inserted, + in_subsystem_edges_inserted, + weak_modularity_finding: weak_modularity_finding_emitted, + clustering_stats: phase3_stats_json( + config, + cluster_result.algorithm_used, + "completed", + None, + graph.modules.len(), + graph.edges.len(), + inserted_subsystems.len(), + Some(cluster_result.modularity_score), + subsystems_inserted, + in_subsystem_edges_inserted, + weak_modularity_finding_emitted, + started, + ), + }) +} + +fn subsystem_entity_id(cluster_hash: &str) -> Result { + Ok(clarion_core::entity_id::entity_id("core", "subsystem", cluster_hash)?.to_string()) +} + +fn subsystem_display_name(member_ids: &[String], cluster_hash: &str) -> (String, String) { + common_module_prefix(member_ids).map_or_else( + || (format!("Subsystem {cluster_hash}"), cluster_hash.to_owned()), + |prefix| (prefix.clone(), prefix), + ) +} + +fn common_module_prefix(member_ids: &[String]) -> Option { + let mut names = member_ids.iter().filter_map(|id| module_qualified_name(id)); + let first = names.next()?; + let mut common = first.split('.').collect::>(); + for name in names { + let parts = name.split('.').collect::>(); + let shared = common + .iter() + .zip(parts.iter()) + .take_while(|(left, right)| left == right) + .count(); + common.truncate(shared); + if common.is_empty() { + return None; + } + } + if common.is_empty() { + None + } else { + Some(common.join(".")) + } +} + +fn module_qualified_name(entity_id: &str) -> Option<&str> { + let mut parts = entity_id.splitn(3, ':'); + let _plugin_id = parts.next()?; + let kind = parts.next()?; + let qualified = parts.next()?; + if kind == "module" && !qualified.is_empty() { + Some(qualified) + } else { + None + } +} + +async fn insert_weak_modularity_finding( + writer: &Writer, + run_id: &str, + config: &ClusteringConfig, + subsystems: &[InsertedSubsystem], + modularity_score: f64, +) -> Result { + let Some(anchor) = subsystems + .iter() + .max_by_key(|subsystem| (subsystem.member_count, std::cmp::Reverse(&subsystem.id))) + else { + return Ok(false); + }; + let subsystem_ids = subsystems + .iter() + .map(|subsystem| subsystem.id.clone()) + .collect::>(); + let now = iso8601_now(); + let finding_id = format!("core:finding:{run_id}:weak-modularity"); + let related_entities_json = serde_json::to_string(&subsystem_ids) + .context("serialize weak modularity related_entities")?; + writer + .send_wait(|ack| WriterCmd::InsertFinding { + finding: Box::new(FindingRecord { + id: finding_id.clone(), + tool: "clarion".to_owned(), + tool_version: env!("CARGO_PKG_VERSION").to_owned(), + run_id: run_id.to_owned(), + rule_id: WEAK_MODULARITY_RULE_ID.to_owned(), + kind: "fact".to_owned(), + severity: "INFO".to_owned(), + confidence: Some(1.0), + confidence_basis: Some("deterministic module graph modularity".to_owned()), + entity_id: anchor.id.clone(), + related_entities_json, + message: "Module graph has weak subsystem modularity".to_owned(), + evidence_json: serde_json::json!({ + "modularity_score": modularity_score, + "threshold": config.weak_modularity_threshold, + "subsystem_count": subsystems.len(), + }) + .to_string(), + properties_json: serde_json::json!({ + "algorithm": config.algorithm.as_str(), + "modularity_score": modularity_score, + "threshold": config.weak_modularity_threshold, + "subsystem_count": subsystems.len(), + }) + .to_string(), + supports_json: "[]".to_owned(), + supported_by_json: "[]".to_owned(), + created_at: now.clone(), + updated_at: now, + }), + ack, + }) + .await + .map_err(|e| anyhow::anyhow!("{e}")) + .with_context(|| format!("InsertFinding {finding_id}"))?; + Ok(true) +} + +fn module_entity_ids(conn: &Connection) -> Result> { + let mut stmt = conn + .prepare("SELECT id FROM entities WHERE kind = 'module' ORDER BY id") + .context("prepare module entity query")?; + let rows = stmt + .query_map([], |row| row.get::<_, String>(0)) + .context("query module entities")?; + rows.collect::, _>>() + .context("collect module entities") +} + +#[allow(clippy::too_many_arguments)] +fn phase3_stats_json( + config: &ClusteringConfig, + algorithm: crate::clustering::ClusterAlgorithm, + status: &str, + skipped_reason: Option<&str>, + module_count: usize, + module_edge_count: usize, + subsystem_count: usize, + modularity_score: Option, + subsystems_inserted: u64, + in_subsystem_edges_inserted: u64, + weak_modularity_finding_emitted: bool, + started: std::time::Instant, +) -> serde_json::Value { + serde_json::json!({ + "enabled": config.enabled, + "algorithm": algorithm.as_str(), + "configured_algorithm": config.algorithm.as_str(), + "status": status, + "seed": config.seed, + "resolution": config.resolution, + "max_iterations": config.max_iterations, + "min_cluster_size": config.min_cluster_size, + "edge_types": config.edge_types.iter().map(|edge_type| edge_type.as_str()).collect::>(), + "weight_by": config.weight_by.as_str(), + "module_count": module_count, + "module_edge_count": module_edge_count, + "subsystem_count": subsystem_count, + "modularity_score": modularity_score, + "duration_ms": u64::try_from(started.elapsed().as_millis()).unwrap_or(u64::MAX), + "subsystems_inserted": subsystems_inserted, + "in_subsystem_edges_inserted": in_subsystem_edges_inserted, + "weak_modularity_threshold": config.weak_modularity_threshold, + "weak_modularity_finding_emitted": weak_modularity_finding_emitted, + "skipped_reason": skipped_reason, + }) +} + // ── Run-outcome ─────────────────────────────────────────────────────────────── // // Three terminal states because plugin crashes and writer-actor failures need @@ -551,9 +1026,11 @@ pub async fn run(project_path: PathBuf) -> Result<()> { // entities that should persist → `CommitRun(Failed)`. The writer folds // `UPDATE runs ... status='failed'` into the open entity transaction so // the batch commits and the run row marks failed atomically. Exit 1. -// - `HardFailed`: writer-actor rejected an `InsertEntity` (DB locked, disk -// full, etc.) → `FailRun`. The writer rolls back the open transaction. -// Exit 1. Continuing past this makes no sense — the DB is unusable. +// - `HardFailed`: the writer rejected a mutation or the Phase 3 pre-flush +// validation rejected the pending graph (DB locked, disk full, +// parent/contains mismatch, etc.) → `FailRun`. The writer rolls back the +// still-open transaction before the run row is marked failed. Exit 1. +// Continuing past this makes no sense — the DB is unusable or inconsistent. #[derive(Debug)] enum RunOutcome { @@ -562,10 +1039,30 @@ enum RunOutcome { HardFailed { reason: String }, } +fn log_plugin_findings(plugin_id: &str, findings: &[HostFinding]) { + if findings.is_empty() { + return; + } + tracing::warn!( + plugin_id = %plugin_id, + finding_count = findings.len(), + "plugin host collected findings" + ); + for f in findings { + tracing::warn!( + plugin_id = %plugin_id, + subcode = %f.subcode, + message = %f.message, + metadata = ?f.metadata, + "plugin host finding", + ); + } +} + // ── JoinError handling ──────────────────────────────────────────────────────── /// Convert a `spawn_blocking` join result into the plugin-crash-shaped -/// `Result` the caller already knows how to handle. +/// `Result` the caller already knows how to handle. /// /// The `Err(JoinError)` arm is the load-bearing one: a panic inside /// `run_plugin_blocking` would otherwise `?`-propagate past the run-outcome @@ -574,9 +1071,9 @@ enum RunOutcome { /// path (ticks the crash-loop breaker, resolves to `SoftFailed` if no writer /// error occurred). fn handle_plugin_task_join_result( - result: Result, tokio::task::JoinError>, + result: Result, tokio::task::JoinError>, plugin_id: &str, -) -> Result { +) -> Result { match result { Ok(inner) => inner, Err(join_err) => { @@ -585,7 +1082,9 @@ fn handle_plugin_task_join_result( error = %join_err, "plugin task panicked; recording as crash", ); - Err(format!("plugin task for {plugin_id} panicked: {join_err}")) + Err(PluginRunError::new(format!( + "plugin task for {plugin_id} panicked: {join_err}" + ))) } } } @@ -608,6 +1107,25 @@ struct BatchResult { findings: Vec, } +#[derive(Debug)] +struct PluginRunError { + reason: String, + findings: Vec, +} + +impl PluginRunError { + fn new(reason: impl Into) -> Self { + Self { + reason: reason.into(), + findings: Vec::new(), + } + } + + fn with_findings(reason: String, findings: Vec) -> Self { + Self { reason, findings } + } +} + #[derive(Debug, Default)] struct BatchStats { unresolved_call_sites_total: u64, @@ -615,8 +1133,11 @@ struct BatchStats { references_resolved_total: u64, references_skipped_external_total: u64, references_skipped_cap_total: u64, + imports_skipped_external_total: u64, unresolved_reference_sites_total: u64, pyright_query_latency_ms: Vec, + pyright_index_parse_latency_ms: Vec, + extractor_parse_latency_ms: Vec, } #[derive(Debug, Clone)] @@ -649,16 +1170,20 @@ fn run_plugin_blocking( plugin_id: &str, executable: &Path, files: &[PathBuf], -) -> Result { +) -> Result { use clarion_core::PluginHost; let (mut host, mut child) = PluginHost::spawn(manifest, project_root, executable).map_err(|e| match e { - HostError::Spawn(msg) => format!("failed to spawn plugin {plugin_id}: {msg}"), + HostError::Spawn(msg) => { + PluginRunError::new(format!("failed to spawn plugin {plugin_id}: {msg}")) + } HostError::Handshake(ref me) => { - format!("plugin {plugin_id} refused handshake: {me}") + PluginRunError::new(format!("plugin {plugin_id} refused handshake: {me}")) + } + other => { + PluginRunError::new(format!("plugin {plugin_id} spawn/handshake error: {other}")) } - other => format!("plugin {plugin_id} spawn/handshake error: {other}"), })?; let work_result: Result = (|| { @@ -685,6 +1210,14 @@ fn run_plugin_blocking( collected_stats .pyright_query_latency_ms .extend(stats.pyright_query_latency_ms.iter().copied()); + collected_stats + .pyright_index_parse_latency_ms + .extend(stats.pyright_index_parse_latency_ms.iter().copied()); + if stats.extractor_parse_latency_ms > 0 { + collected_stats + .extractor_parse_latency_ms + .push(stats.extractor_parse_latency_ms); + } let source_file_id = entities .iter() .find(|entity| entity.kind == "module") @@ -715,6 +1248,8 @@ fn run_plugin_blocking( collected_edges.push((descr, record)); } } + collected_stats.imports_skipped_external_total += + filter_external_import_edges(&collected_entities, &mut collected_edges); Ok(( collected_entities, collected_edges, @@ -742,6 +1277,7 @@ fn run_plugin_blocking( } let mut findings = host.take_findings(); + drop(host); // Reap unconditionally. `Child::Drop` does not wait on Unix. reap_and_classify_exit(&mut child, plugin_id, &mut findings); @@ -754,7 +1290,7 @@ fn run_plugin_blocking( stats, findings, }), - Err(reason) => Err(reason), + Err(reason) => Err(PluginRunError::with_findings(reason, findings)), } } @@ -771,39 +1307,46 @@ fn reap_and_classify_exit( plugin_id: &str, findings: &mut Vec, ) { - match child.wait() { - Ok(status) if !status.success() => { - #[cfg(unix)] - { - use std::os::unix::process::ExitStatusExt; - if let Some(signal) = status.signal() { - tracing::warn!( - plugin_id = %plugin_id, - signal, - "plugin terminated by signal", - ); - // SIGKILL (9) and SIGSEGV (11) are the observed signatures - // of an RLIMIT_AS kill in Sprint-1 testing. - if signal == 9 || signal == 11 { - findings.push(HostFinding::oom_killed(plugin_id, signal)); - } - } else if let Some(code) = status.code() { - tracing::warn!( - plugin_id = %plugin_id, - code, - "plugin exited non-zero", - ); - } - } - #[cfg(not(unix))] - { + reap_and_classify_exit_with_timeout(child, plugin_id, findings, PLUGIN_REAP_TIMEOUT); +} + +const PLUGIN_REAP_TIMEOUT: std::time::Duration = std::time::Duration::from_secs(5); +const PLUGIN_REAP_POLL_INTERVAL: std::time::Duration = std::time::Duration::from_millis(20); + +fn reap_and_classify_exit_with_timeout( + child: &mut std::process::Child, + plugin_id: &str, + findings: &mut Vec, + timeout: std::time::Duration, +) { + match wait_child_with_timeout(child, timeout) { + Ok(Some(status)) => classify_child_exit_status(status, plugin_id, findings), + Ok(None) => { + tracing::warn!( + plugin_id = %plugin_id, + timeout_ms = timeout.as_millis(), + "plugin did not exit before reap timeout; killing child", + ); + if let Err(e) = child.kill() { tracing::warn!( plugin_id = %plugin_id, - "plugin exited non-successfully (exit-status inspection is Unix-only)", + error = %e, + "failed to kill plugin child after reap timeout", ); } + match child.wait() { + Ok(status) => tracing::warn!( + plugin_id = %plugin_id, + status = ?status, + "plugin child reaped after timeout kill", + ), + Err(e) => tracing::warn!( + plugin_id = %plugin_id, + error = %e, + "failed to wait on plugin child after timeout kill", + ), + } } - Ok(_) => {} // clean exit Err(e) => { tracing::warn!( plugin_id = %plugin_id, @@ -814,6 +1357,62 @@ fn reap_and_classify_exit( } } +fn wait_child_with_timeout( + child: &mut std::process::Child, + timeout: std::time::Duration, +) -> std::io::Result> { + let deadline = std::time::Instant::now() + timeout; + loop { + if let Some(status) = child.try_wait()? { + return Ok(Some(status)); + } + let now = std::time::Instant::now(); + if now >= deadline { + return Ok(None); + } + std::thread::sleep(PLUGIN_REAP_POLL_INTERVAL.min(deadline - now)); + } +} + +fn classify_child_exit_status( + status: std::process::ExitStatus, + plugin_id: &str, + findings: &mut Vec, +) { + if status.success() { + return; + } + #[cfg(unix)] + { + use std::os::unix::process::ExitStatusExt; + if let Some(signal) = status.signal() { + tracing::warn!( + plugin_id = %plugin_id, + signal, + "plugin terminated by signal", + ); + // SIGKILL (9) and SIGSEGV (11) are the observed signatures + // of an RLIMIT_AS kill in Sprint-1 testing. + if signal == 9 || signal == 11 { + findings.push(HostFinding::oom_killed(plugin_id, signal)); + } + } else if let Some(code) = status.code() { + tracing::warn!( + plugin_id = %plugin_id, + code, + "plugin exited non-zero", + ); + } + } + #[cfg(not(unix))] + { + tracing::warn!( + plugin_id = %plugin_id, + "plugin exited non-successfully (exit-status inspection is Unix-only)", + ); + } +} + /// Map a `HostError` from `analyze_file` to a human-readable fail-run reason. fn classify_host_error(plugin_id: &str, e: HostError) -> String { match e { @@ -842,6 +1441,61 @@ fn classify_host_error(plugin_id: &str, e: HostError) -> String { } } +fn filter_external_import_edges( + entities: &[(String, EntityRecord)], + edges: &mut Vec<(String, EdgeRecord)>, +) -> u64 { + let module_entity_ids: BTreeSet<&str> = entities + .iter() + .filter(|(_, record)| record.kind == "module") + .map(|(id, _)| id.as_str()) + .collect(); + let before = edges.len(); + edges.retain_mut(|(_, edge)| { + if edge.kind != "imports" { + return true; + } + if let Some(local_submodule) = + absolute_from_import_submodule_target(edge, &module_entity_ids) + { + edge.to_id = local_submodule; + return true; + } + module_entity_ids.contains(edge.to_id.as_str()) + }); + u64::try_from(before - edges.len()).unwrap_or(u64::MAX) +} + +fn absolute_from_import_submodule_target( + edge: &EdgeRecord, + module_entity_ids: &BTreeSet<&str>, +) -> Option { + let properties = edge + .properties_json + .as_deref() + .and_then(|raw| serde_json::from_str::(raw).ok())?; + if properties + .get("import_style") + .and_then(|value| value.as_str()) + != Some("from_import") + { + return None; + } + if properties.get("level").and_then(serde_json::Value::as_u64) != Some(0) { + return None; + } + let imported_name = properties + .get("imported_name") + .and_then(|value| value.as_str())?; + if imported_name == "*" || imported_name.is_empty() { + return None; + } + let candidate = format!("{}.{}", edge.to_id, imported_name); + module_entity_ids + .contains(candidate.as_str()) + .then_some(candidate) +} + /// Map an `AcceptedEntity` to an `EntityRecord` for the writer-actor. fn map_entity_to_record( entity: &AcceptedEntity, @@ -1073,9 +1727,9 @@ const SKIP_DIRS: &[&str] = &[ /// Collect all source files under `root` whose extension is in `wanted`. /// -/// Uses `std::fs::read_dir` recursively. No `walkdir` dependency. -/// Symlinks are skipped (path-jail concerns for Sprint 1). -/// P4 observation: this does not respect `.gitignore`. +/// Uses the `ignore` crate so `.gitignore` / `.ignore` / global gitignore +/// policy filters the source set before plugin dispatch. Symlinks are skipped +/// (path-jail concerns for Sprint 1). /// /// Per-entry I/O errors (a dirent we couldn't stat, a file whose /// `file_type()` probe failed) are logged at `warn` level and counted. @@ -1083,13 +1737,48 @@ const SKIP_DIRS: &[&str] = &[ /// the operator can see that the file list is incomplete — silently /// dropping those entries would mask the same "incomplete analysis" /// class that the WP1 `read_applied_versions` `.ok()` pattern did. -fn collect_source_files( - root: &Path, - wanted_extensions: &BTreeSet, -) -> io::Result> { +fn collect_source_files(root: &Path, wanted_extensions: &BTreeSet) -> Vec { let mut out = Vec::new(); let mut skipped: u64 = 0; - walk_dir(root, &mut out, &mut skipped, wanted_extensions)?; + let mut builder = WalkBuilder::new(root); + builder + .follow_links(false) + .hidden(false) + .ignore(true) + .git_ignore(true) + .git_global(true) + .git_exclude(true) + .parents(true) + .require_git(false) + .filter_entry(|entry| !is_skipped_dir(entry)); + + for result in builder.build() { + match result { + Ok(entry) => { + let Some(file_type) = entry.file_type() else { + continue; + }; + if !file_type.is_file() { + continue; + } + let path = entry.into_path(); + if let Some(ext) = path.extension().and_then(|e| e.to_str()) { + let ext_lower = ext.to_ascii_lowercase(); + if wanted_extensions.contains(&ext_lower) { + out.push(path); + } + } + } + Err(err) => { + tracing::warn!( + error = %err, + "source walk: skipping unreadable or ignored-path-error entry", + ); + skipped += 1; + } + } + } + if skipped > 0 { tracing::warn!( skipped = skipped, @@ -1099,124 +1788,30 @@ fn collect_source_files( suffix = if skipped == 1 { "y" } else { "ies" }, ); } - Ok(out) + out } -fn walk_dir( - dir: &Path, - out: &mut Vec, - skipped: &mut u64, - wanted: &BTreeSet, -) -> io::Result<()> { - let entries = match std::fs::read_dir(dir) { - Ok(e) => e, - Err(e) if e.kind() == io::ErrorKind::PermissionDenied => return Ok(()), - Err(e) => return Err(e), - }; - - for entry_result in entries { - let entry = match entry_result { - Ok(entry) => entry, - Err(e) => { - tracing::warn!( - error = %e, - dir = %dir.display(), - "source walk: skipping unreadable directory entry", - ); - *skipped += 1; - continue; - } - }; - let file_type = match entry.file_type() { - Ok(ft) => ft, - Err(e) => { - tracing::warn!( - error = %e, - path = %entry.path().display(), - "source walk: skipping entry whose file_type() probe failed", - ); - *skipped += 1; - continue; - } - }; - - // Skip symlinks (path-jail concerns). - if file_type.is_symlink() { - continue; - } - - let path = entry.path(); - - if file_type.is_dir() { - // Skip directories in the skip-list. - let dir_name = entry.file_name(); - let name_str = dir_name.to_string_lossy(); - if SKIP_DIRS.iter().any(|skip| *skip == name_str.as_ref()) { - continue; - } - walk_dir(&path, out, skipped, wanted)?; - } else if file_type.is_file() { - // Check extension (case-insensitive compare; `wanted` is already lowercase). - if let Some(ext) = path.extension().and_then(|e| e.to_str()) { - let ext_lower = ext.to_ascii_lowercase(); - if wanted.contains(&ext_lower) { - out.push(path); - } - } - } - } - - Ok(()) +fn is_skipped_dir(entry: &DirEntry) -> bool { + entry + .file_type() + .is_some_and(|file_type| file_type.is_dir()) + && entry + .file_name() + .to_str() + .is_some_and(|name| SKIP_DIRS.contains(&name)) } // ── Time helpers ────────────────────────────────────────────────────────────── -/// Format `SystemTime::now()` as an `ISO-8601` UTC string with millisecond -/// precision (`YYYY-MM-DDTHH:MM:SS.sssZ`). -/// -/// Inline rather than depending on `chrono` — Sprint 1 only needs this one -/// formatting pattern. Later WPs that want richer time handling can -/// promote `chrono` to a workspace dependency at that point. -fn iso8601_now() -> String { - use std::time::{SystemTime, UNIX_EPOCH}; - let d = SystemTime::now() - .duration_since(UNIX_EPOCH) - .expect("SystemTime before UNIX epoch"); - let secs = d.as_secs(); - let millis = d.subsec_millis(); - let (y, mo, da, h, mi, se) = civil_from_unix_secs(secs); - format!("{y:04}-{mo:02}-{da:02}T{h:02}:{mi:02}:{se:02}.{millis:03}Z") -} +const ISO8601_MILLIS_UTC: &[time::format_description::FormatItem<'_>] = + format_description!("[year]-[month]-[day]T[hour]:[minute]:[second].[subsecond digits:3]Z"); -/// Convert a non-negative Unix timestamp (seconds since 1970-01-01 UTC) -/// into `(year, month, day, hour, minute, second)`. -/// -/// Algorithm: Howard Hinnant's date, `civil_from_days`. Works for any date -/// from the Unix epoch forward. Does not account for leap seconds (none -/// of our timestamps need leap-second precision). -fn civil_from_unix_secs(mut secs: u64) -> (u32, u32, u32, u32, u32, u32) { - let se = u32::try_from(secs % 60).expect("modulo 60 fits in u32"); - secs /= 60; - let mi = u32::try_from(secs % 60).expect("modulo 60 fits in u32"); - secs /= 60; - let h = u32::try_from(secs % 24).expect("modulo 24 fits in u32"); - secs /= 24; - - // secs is now days since the Unix epoch (1970-01-01). - // Howard Hinnant's algorithm needs days shifted to 0000-03-01 epoch. - let days = i64::try_from(secs).expect("days since epoch fits in i64"); - let z = days + 719_468; - let era = if z >= 0 { z } else { z - 146_096 } / 146_097; - let doe = u64::try_from(z - era * 146_097).expect("day-of-era is non-negative"); - let yoe = (doe - doe / 1460 + doe / 36524 - doe / 146_096) / 365; - let y_shifted = i64::try_from(yoe).expect("year-of-era fits in i64") + era * 400; - let doy = doe - (365 * yoe + yoe / 4 - yoe / 100); - let mp = (5 * doy + 2) / 153; - let da = u32::try_from(doy - (153 * mp + 2) / 5 + 1).expect("day-of-month fits in u32"); - let mo = u32::try_from(if mp < 10 { mp + 3 } else { mp - 9 }).expect("month fits in u32"); - let y_i64 = if mo <= 2 { y_shifted + 1 } else { y_shifted }; - let y = u32::try_from(y_i64).expect("year fits in u32 (post-1970)"); - (y, mo, da, h, mi, se) +/// Format `OffsetDateTime::now_utc()` as an `ISO-8601` UTC string with +/// millisecond precision (`YYYY-MM-DDTHH:MM:SS.sssZ`). +fn iso8601_now() -> String { + OffsetDateTime::now_utc() + .format(ISO8601_MILLIS_UTC) + .expect("fixed ISO-8601 format description should format") } // ── Tests ───────────────────────────────────────────────────────────────────── @@ -1224,6 +1819,213 @@ fn civil_from_unix_secs(mut secs: u64) -> (u32, u32, u32, u32, u32, u32) { #[cfg(test)] mod tests { use super::*; + use std::collections::BTreeSet; + use std::fs; + + #[test] + fn subsystem_entity_id_rejects_invalid_hash_segment() { + let err = subsystem_entity_id("bad:hash").expect_err("colon must be rejected"); + + assert!( + err.to_string() + .contains("canonical_qualified_name contains reserved ':' separator"), + "unexpected error: {err:#}" + ); + } + + #[test] + fn source_walk_honours_root_gitignore() { + let tempdir = tempfile::tempdir().expect("tempdir"); + let root = tempdir.path(); + fs::write(root.join(".gitignore"), "ignored/\n*.generated.py\n").expect("gitignore"); + fs::write(root.join("kept.py"), "print('kept')\n").expect("kept source"); + fs::write(root.join("skip.generated.py"), "print('ignored pattern')\n") + .expect("ignored source"); + fs::create_dir(root.join("ignored")).expect("ignored dir"); + fs::write(root.join("ignored").join("hidden.py"), "print('hidden')\n") + .expect("ignored dir source"); + + let wanted = BTreeSet::from(["py".to_owned()]); + let mut files = collect_source_files(root, &wanted); + files.sort(); + let relative = files + .into_iter() + .map(|path| { + path.strip_prefix(root) + .expect("under temp root") + .to_string_lossy() + .replace('\\', "/") + }) + .collect::>(); + + assert_eq!(relative, vec!["kept.py"]); + } + + #[test] + fn filter_import_edges_prefers_absolute_from_import_submodule_when_local() { + let entities = vec![ + module_record("python:module:pkg"), + module_record("python:module:pkg.service"), + ]; + let mut edges = vec![from_import_edge( + "python:module:consumer", + "python:module:pkg", + "service", + )]; + + let skipped = filter_external_import_edges(&entities, &mut edges); + + assert_eq!(skipped, 0); + assert_eq!(edges[0].1.to_id, "python:module:pkg.service"); + } + + #[test] + fn filter_import_edges_keeps_parent_for_absolute_from_import_reexport() { + let entities = vec![module_record("python:module:pkg")]; + let mut edges = vec![from_import_edge( + "python:module:consumer", + "python:module:pkg", + "helper", + )]; + + let skipped = filter_external_import_edges(&entities, &mut edges); + + assert_eq!(skipped, 0); + assert_eq!(edges[0].1.to_id, "python:module:pkg"); + } + + #[test] + fn filter_import_edges_accepts_namespace_package_submodule() { + let entities = vec![module_record("python:module:pkg.service")]; + let mut edges = vec![from_import_edge( + "python:module:consumer", + "python:module:pkg", + "service", + )]; + + let skipped = filter_external_import_edges(&entities, &mut edges); + + assert_eq!(skipped, 0); + assert_eq!(edges[0].1.to_id, "python:module:pkg.service"); + } + + #[test] + fn filter_import_edges_counts_only_truly_external_imports() { + let entities = vec![module_record("python:module:consumer")]; + let mut edges = vec![from_import_edge( + "python:module:consumer", + "python:module:external", + "service", + )]; + + let skipped = filter_external_import_edges(&entities, &mut edges); + + assert_eq!(skipped, 1); + assert!(edges.is_empty()); + } + + #[test] + fn subsystem_display_name_uses_common_module_prefix() { + let (name, short_name) = subsystem_display_name( + &[ + "python:module:pkg.auth.login".to_owned(), + "python:module:pkg.auth.policy".to_owned(), + "python:module:pkg.auth.token".to_owned(), + ], + "abc123def456", + ); + + assert_eq!(name, "pkg.auth"); + assert_eq!(short_name, "pkg.auth"); + } + + #[test] + fn subsystem_display_name_falls_back_to_hash_without_common_prefix() { + let (name, short_name) = subsystem_display_name( + &[ + "python:module:auth.login".to_owned(), + "python:module:billing.invoice".to_owned(), + ], + "abc123def456", + ); + + assert_eq!(name, "Subsystem abc123def456"); + assert_eq!(short_name, "abc123def456"); + } + + #[test] + fn phase3_stats_distinguishes_configured_and_used_algorithm() { + let config = AnalyzeConfig::default().analysis.clustering; + + let stats = phase3_stats_json( + &config, + crate::clustering::ClusterAlgorithm::WeightedComponents, + "completed", + None, + 3, + 2, + 2, + Some(0.5), + 2, + 3, + false, + std::time::Instant::now(), + ); + + assert_eq!(stats["configured_algorithm"].as_str(), Some("leiden")); + assert_eq!(stats["algorithm"].as_str(), Some("weighted_components")); + } + + fn module_record(id: &str) -> (String, EntityRecord) { + ( + id.to_owned(), + EntityRecord { + id: id.to_owned(), + plugin_id: "python".to_owned(), + kind: "module".to_owned(), + name: id.trim_start_matches("python:module:").to_owned(), + short_name: id.rsplit('.').next().unwrap_or(id).to_owned(), + parent_id: None, + source_file_id: None, + source_file_path: None, + source_byte_start: None, + source_byte_end: None, + source_line_start: None, + source_line_end: None, + properties_json: "{}".to_owned(), + content_hash: None, + summary_json: None, + wardline_json: None, + first_seen_commit: None, + last_seen_commit: None, + created_at: "2026-05-17T00:00:00.000Z".to_owned(), + updated_at: "2026-05-17T00:00:00.000Z".to_owned(), + }, + ) + } + + fn from_import_edge(from_id: &str, to_id: &str, imported_name: &str) -> (String, EdgeRecord) { + ( + format!("imports {from_id} -> {to_id}"), + EdgeRecord { + kind: "imports".to_owned(), + from_id: from_id.to_owned(), + to_id: to_id.to_owned(), + confidence: clarion_core::EdgeConfidence::Resolved, + properties_json: Some( + serde_json::json!({ + "imported_name": imported_name, + "import_style": "from_import", + "level": 0 + }) + .to_string(), + ), + source_file_id: Some(from_id.to_owned()), + source_byte_start: Some(0), + source_byte_end: Some(10), + }, + ) + } // ── handle_plugin_task_join_result ──────────────────────────────────────── // @@ -1250,10 +2052,15 @@ mod tests { #[test] fn handle_task_passes_through_ok_err() { - let out = - handle_plugin_task_join_result(Ok(Err("spawn failed: ENOENT".to_owned())), "python"); + let out = handle_plugin_task_join_result( + Ok(Err(PluginRunError::new("spawn failed: ENOENT"))), + "python", + ); match out { - Err(s) => assert_eq!(s, "spawn failed: ENOENT"), + Err(e) => { + assert_eq!(e.reason, "spawn failed: ENOENT"); + assert!(e.findings.is_empty()); + } Ok(_) => panic!("expected Err pass-through"), } } @@ -1263,7 +2070,7 @@ mod tests { // Drive a real JoinError through the helper by panicking inside // spawn_blocking. Asserting on the structure-of-Err (not the exact // message) so this stays robust across tokio's internal formatting. - let join_result = tokio::task::spawn_blocking(|| -> Result { + let join_result = tokio::task::spawn_blocking(|| -> Result { panic!("simulated plugin-task panic"); }) .await; @@ -1273,16 +2080,49 @@ mod tests { ); let out = handle_plugin_task_join_result(join_result, "python"); match out { - Err(s) => { + Err(e) => { assert!( - s.contains("plugin task for python panicked"), - "reason must identify plugin_id; got: {s}" + e.reason.contains("plugin task for python panicked"), + "reason must identify plugin_id; got: {}", + e.reason ); + assert!(e.findings.is_empty()); } Ok(_) => panic!("JoinError must convert to Err, not Ok"), } } + #[test] + #[cfg(unix)] + fn reap_timeout_kills_stubborn_child() { + let mut child = std::process::Command::new("sleep") + .arg("60") + .spawn() + .expect("spawn sleeping child"); + let mut findings = Vec::new(); + let start = std::time::Instant::now(); + + reap_and_classify_exit_with_timeout( + &mut child, + "stubborn", + &mut findings, + std::time::Duration::from_millis(50), + ); + + assert!( + start.elapsed() < std::time::Duration::from_secs(2), + "bounded reap should not wait for the child sleep" + ); + assert!( + child.try_wait().expect("query child status").is_some(), + "timed-out child should be killed and reaped" + ); + assert!( + findings.is_empty(), + "timeout kill should not be misclassified as an OOM finding: {findings:?}" + ); + } + #[test] fn map_entity_persists_source_metadata_and_content_hash() { let tempdir = tempfile::tempdir().unwrap(); diff --git a/crates/clarion-cli/src/cli.rs b/crates/clarion-cli/src/cli.rs index 351a3812..859631e8 100644 --- a/crates/clarion-cli/src/cli.rs +++ b/crates/clarion-cli/src/cli.rs @@ -13,7 +13,7 @@ pub struct Cli { pub enum Command { /// Initialise .clarion/ in the current directory. Install { - /// Overwrite an existing .clarion/ (not implemented in Sprint 1). + /// Overwrite an existing .clarion/ directory. #[arg(long)] force: bool, @@ -28,6 +28,10 @@ pub enum Command { /// Path to analyse (default: current directory). #[arg(default_value = ".")] path: PathBuf, + + /// Path to clarion.yaml (default: project-root/clarion.yaml if present). + #[arg(long)] + config: Option, }, /// Run the MCP stdio server. diff --git a/crates/clarion-cli/src/clustering.rs b/crates/clarion-cli/src/clustering.rs new file mode 100644 index 00000000..97b043e0 --- /dev/null +++ b/crates/clarion-cli/src/clustering.rs @@ -0,0 +1,510 @@ +use anyhow::{Context, Result, ensure}; +use serde::{Deserialize, Serialize}; +use sha2::{Digest, Sha256}; +use std::collections::{BTreeMap, BTreeSet, HashMap}; +use xgraph::graph::algorithms::leiden_clustering::{CommunityConfig, CommunityDetection}; +use xgraph::graph::graph::Graph; + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "snake_case")] +pub(crate) enum ClusterAlgorithm { + Leiden, + WeightedComponents, +} + +impl ClusterAlgorithm { + pub(crate) fn as_str(self) -> &'static str { + match self { + ClusterAlgorithm::Leiden => "leiden", + ClusterAlgorithm::WeightedComponents => "weighted_components", + } + } +} + +#[derive(Debug, Clone, PartialEq, Eq)] +pub(crate) struct ModuleEdge { + pub(crate) from: String, + pub(crate) to: String, + pub(crate) reference_count: u64, +} + +#[derive(Debug, Clone, PartialEq, Eq)] +pub(crate) struct ModuleGraph { + pub(crate) modules: Vec, + pub(crate) edges: Vec, +} + +#[derive(Debug, Clone, PartialEq)] +pub(crate) struct ClusterConfig { + pub(crate) algorithm: ClusterAlgorithm, + pub(crate) seed: u64, + pub(crate) resolution: f64, + pub(crate) max_iterations: u32, + pub(crate) min_cluster_size: usize, +} + +#[derive(Debug, Clone, PartialEq)] +pub(crate) struct ClusterResult { + pub(crate) communities: Vec>, + pub(crate) modularity_score: f64, + pub(crate) algorithm_used: ClusterAlgorithm, +} + +pub(crate) fn cluster_modules( + graph: &ModuleGraph, + config: &ClusterConfig, +) -> Result { + cluster_modules_with_algorithms(graph, config, leiden_communities, local_weighted_components) +} + +fn cluster_modules_with_algorithms( + graph: &ModuleGraph, + config: &ClusterConfig, + leiden: impl FnOnce(&ModuleGraph, &ClusterConfig) -> Result>>, + mut weighted_components: impl FnMut(&ModuleGraph, usize) -> Vec>, +) -> Result { + ensure!( + config.max_iterations > 0, + "clustering max_iterations must be greater than zero" + ); + ensure!( + config.resolution.is_finite() && config.resolution > 0.0, + "clustering resolution must be a positive finite number" + ); + + let (mut communities, algorithm_used) = match config.algorithm { + ClusterAlgorithm::Leiden => { + let communities = leiden(graph, config)?; + if communities.len() <= 1 { + let fallback = weighted_components(graph, config.min_cluster_size); + if fallback.len() > communities.len() { + (fallback, ClusterAlgorithm::WeightedComponents) + } else { + (communities, ClusterAlgorithm::Leiden) + } + } else { + (communities, ClusterAlgorithm::Leiden) + } + } + ClusterAlgorithm::WeightedComponents => ( + weighted_components(graph, config.min_cluster_size), + ClusterAlgorithm::WeightedComponents, + ), + }; + normalize_communities(&mut communities); + + Ok(ClusterResult { + modularity_score: directed_modularity(graph, &communities), + communities, + algorithm_used, + }) +} + +pub(crate) fn cluster_hash(member_ids: &[String]) -> String { + let mut sorted = member_ids.to_vec(); + sorted.sort(); + + let mut hasher = Sha256::new(); + for member_id in sorted { + hasher.update(member_id.as_bytes()); + } + format!("{:x}", hasher.finalize()) + .chars() + .take(12) + .collect() +} + +fn leiden_communities(graph: &ModuleGraph, config: &ClusterConfig) -> Result>> { + if graph.modules.is_empty() { + return Ok(Vec::new()); + } + + let (xgraph, module_ids) = xgraph_projection(graph)?; + let raw = xgraph + .detect_communities_with_config(CommunityConfig { + gamma: config.resolution, + resolution: config.resolution, + iterations: config.max_iterations as usize, + deterministic: true, + seed: Some(config.seed), + }) + .context("run xgraph Leiden community detection")?; + + let communities = raw + .into_values() + .map(|nodes| { + nodes + .into_iter() + .filter_map(|node| module_ids.get(node).cloned()) + .collect::>() + }) + .filter(|community| community.len() >= config.min_cluster_size) + .collect(); + + Ok(communities) +} + +fn xgraph_projection(graph: &ModuleGraph) -> Result<(Graph, Vec)> { + let mut module_ids = graph.modules.clone(); + module_ids.sort(); + module_ids.dedup(); + + let mut projected = Graph::::new(true); + let node_ids = module_ids + .iter() + .map(|module_id| (module_id.clone(), projected.add_node(module_id.clone()))) + .collect::>(); + + for edge in &graph.edges { + let (Some(from), Some(to)) = (node_ids.get(&edge.from), node_ids.get(&edge.to)) else { + continue; + }; + projected + .add_edge(*from, *to, reference_weight(edge.reference_count), ()) + .context("project module dependency edge into xgraph")?; + } + + Ok((projected, module_ids)) +} + +fn local_weighted_components(graph: &ModuleGraph, min_cluster_size: usize) -> Vec> { + if graph.modules.is_empty() { + return Vec::new(); + } + + let threshold = average_positive_weight(graph).max(1.0); + let modules = graph.modules.iter().cloned().collect::>(); + let mut neighbors = modules + .iter() + .map(|module_id| (module_id.clone(), BTreeSet::new())) + .collect::>(); + + for edge in &graph.edges { + if reference_weight(edge.reference_count) >= threshold + && modules.contains(&edge.from) + && modules.contains(&edge.to) + { + neighbors + .entry(edge.from.clone()) + .or_default() + .insert(edge.to.clone()); + neighbors + .entry(edge.to.clone()) + .or_default() + .insert(edge.from.clone()); + } + } + + let mut seen = BTreeSet::new(); + let mut communities = Vec::new(); + for module_id in modules { + if !seen.insert(module_id.clone()) { + continue; + } + + let mut stack = vec![module_id]; + let mut community = Vec::new(); + while let Some(current) = stack.pop() { + community.push(current.clone()); + if let Some(next) = neighbors.get(¤t) { + for neighbor in next.iter().rev() { + if seen.insert(neighbor.clone()) { + stack.push(neighbor.clone()); + } + } + } + } + community.sort(); + if community.len() >= min_cluster_size { + communities.push(community); + } + } + + communities +} + +fn average_positive_weight(graph: &ModuleGraph) -> f64 { + let positive = graph + .edges + .iter() + .filter(|edge| edge.reference_count > 0) + .map(|edge| reference_weight(edge.reference_count)) + .collect::>(); + if positive.is_empty() { + 1.0 + } else { + positive.iter().sum::() / usize_to_f64(positive.len()) + } +} + +fn normalize_communities(communities: &mut [Vec]) { + for community in communities.iter_mut() { + community.sort(); + } + communities.sort(); +} + +fn directed_modularity(graph: &ModuleGraph, communities: &[Vec]) -> f64 { + let total_weight = graph + .edges + .iter() + .map(|edge| reference_weight(edge.reference_count)) + .sum::(); + if total_weight <= f64::EPSILON || communities.is_empty() { + return 0.0; + } + + let community_by_module = communities + .iter() + .enumerate() + .flat_map(|(community_idx, community)| { + community + .iter() + .cloned() + .map(move |member| (member, community_idx)) + }) + .collect::>(); + + let mut out_weight = HashMap::<&str, f64>::new(); + let mut in_weight = HashMap::<&str, f64>::new(); + for edge in &graph.edges { + *out_weight.entry(edge.from.as_str()).or_default() += + reference_weight(edge.reference_count); + *in_weight.entry(edge.to.as_str()).or_default() += reference_weight(edge.reference_count); + } + + let mut modularity = 0.0; + for edge in &graph.edges { + let (Some(from_community), Some(to_community)) = ( + community_by_module.get(&edge.from), + community_by_module.get(&edge.to), + ) else { + continue; + }; + if from_community == to_community { + let expected = out_weight + .get(edge.from.as_str()) + .copied() + .unwrap_or_default() + * in_weight.get(edge.to.as_str()).copied().unwrap_or_default() + / total_weight; + modularity += reference_weight(edge.reference_count) - expected; + } + } + + modularity / total_weight +} + +fn reference_weight(reference_count: u64) -> f64 { + // Module dependency weights are reference counts; cap at u32::MAX before + // floating-point projection so clustering math remains warning-clean and + // deterministic without pretending f64 can exactly represent all u64s. + f64::from(u32::try_from(reference_count).unwrap_or(u32::MAX)) +} + +fn usize_to_f64(value: usize) -> f64 { + f64::from(u32::try_from(value).unwrap_or(u32::MAX)) +} + +#[cfg(test)] +mod tests { + use super::*; + + fn config(algorithm: ClusterAlgorithm) -> ClusterConfig { + ClusterConfig { + algorithm, + seed: 42, + resolution: 1.0, + max_iterations: 100, + min_cluster_size: 2, + } + } + + fn sample_graph() -> ModuleGraph { + ModuleGraph { + modules: ids(&[ + "python:module:pkg.auth.login", + "python:module:pkg.auth.token", + "python:module:pkg.billing.invoice", + "python:module:pkg.billing.ledger", + ]), + edges: vec![ + edge( + "python:module:pkg.auth.login", + "python:module:pkg.auth.token", + 16, + ), + edge( + "python:module:pkg.auth.token", + "python:module:pkg.auth.login", + 14, + ), + edge( + "python:module:pkg.billing.invoice", + "python:module:pkg.billing.ledger", + 17, + ), + edge( + "python:module:pkg.billing.ledger", + "python:module:pkg.billing.invoice", + 13, + ), + edge( + "python:module:pkg.auth.login", + "python:module:pkg.billing.invoice", + 1, + ), + ], + } + } + + fn ids(values: &[&str]) -> Vec { + values.iter().map(|value| (*value).to_owned()).collect() + } + + fn edge(from: &str, to: &str, reference_count: u64) -> ModuleEdge { + ModuleEdge { + from: from.to_owned(), + to: to.to_owned(), + reference_count, + } + } + + fn sorted_communities(result: &ClusterResult) -> Vec> { + let mut communities = result.communities.clone(); + for community in &mut communities { + community.sort(); + } + communities.sort(); + communities + } + + fn same_cluster(result: &ClusterResult, left: &str, right: &str) -> bool { + result + .communities + .iter() + .any(|community| contains(community, left) && contains(community, right)) + } + + fn contains(community: &[String], module_id: &str) -> bool { + community.iter().any(|member| member == module_id) + } + + #[test] + fn fixed_seed_leiden_is_byte_stable() { + let graph = sample_graph(); + let cfg = config(ClusterAlgorithm::Leiden); + + let first = cluster_modules(&graph, &cfg).expect("first clustering run"); + let second = cluster_modules(&graph, &cfg).expect("second clustering run"); + + assert_eq!(first.algorithm_used, ClusterAlgorithm::Leiden); + assert_eq!(second.algorithm_used, ClusterAlgorithm::Leiden); + assert_eq!(sorted_communities(&first), sorted_communities(&second)); + assert!((first.modularity_score - second.modularity_score).abs() < f64::EPSILON); + } + + #[test] + fn directed_weighted_edges_affect_partition() { + let result = + cluster_modules(&sample_graph(), &config(ClusterAlgorithm::Leiden)).expect("clusters"); + + assert!(same_cluster( + &result, + "python:module:pkg.auth.login", + "python:module:pkg.auth.token" + )); + assert!(same_cluster( + &result, + "python:module:pkg.billing.invoice", + "python:module:pkg.billing.ledger" + )); + assert!(!same_cluster( + &result, + "python:module:pkg.auth.login", + "python:module:pkg.billing.invoice" + )); + } + + #[test] + fn leiden_auto_fallback_reports_local_weighted_algorithm() { + let graph = sample_graph(); + let one_cluster = graph.modules.clone(); + + let result = cluster_modules_with_algorithms( + &graph, + &config(ClusterAlgorithm::Leiden), + |_graph, _config| Ok(vec![one_cluster]), + local_weighted_components, + ) + .expect("clusters"); + + assert_eq!(result.algorithm_used, ClusterAlgorithm::WeightedComponents); + assert_eq!(result.communities.len(), 2); + assert!(same_cluster( + &result, + "python:module:pkg.auth.login", + "python:module:pkg.auth.token" + )); + assert!(same_cluster( + &result, + "python:module:pkg.billing.invoice", + "python:module:pkg.billing.ledger" + )); + } + + #[test] + fn leiden_with_multiple_communities_does_not_compute_local_weighted_algorithm() { + let graph = sample_graph(); + let result = cluster_modules_with_algorithms( + &graph, + &config(ClusterAlgorithm::Leiden), + |_graph, _config| { + Ok(vec![ + ids(&[ + "python:module:pkg.auth.login", + "python:module:pkg.auth.token", + ]), + ids(&[ + "python:module:pkg.billing.invoice", + "python:module:pkg.billing.ledger", + ]), + ]) + }, + |_graph, _min_cluster_size| { + panic!("weighted-components fallback should not be computed") + }, + ) + .expect("clusters"); + + assert_eq!(result.algorithm_used, ClusterAlgorithm::Leiden); + assert_eq!(result.communities.len(), 2); + } + + #[test] + fn weighted_components_fallback_is_config_selectable() { + let result = cluster_modules( + &sample_graph(), + &config(ClusterAlgorithm::WeightedComponents), + ) + .expect("clusters"); + + assert_eq!(result.algorithm_used, ClusterAlgorithm::WeightedComponents); + assert!(same_cluster( + &result, + "python:module:pkg.auth.login", + "python:module:pkg.auth.token" + )); + } + + #[test] + fn cluster_hash_uses_sha256_sorted_member_ids_truncated_to_12() { + let member_ids = ids(&[ + "python:module:pkg.c", + "python:module:pkg.a", + "python:module:pkg.b", + ]); + + assert_eq!(cluster_hash(&member_ids), "284892d1d0b1"); + } +} diff --git a/crates/clarion-cli/src/config.rs b/crates/clarion-cli/src/config.rs new file mode 100644 index 00000000..74500cce --- /dev/null +++ b/crates/clarion-cli/src/config.rs @@ -0,0 +1,141 @@ +use std::fs; +use std::path::Path; + +use anyhow::{Context, Result, bail, ensure}; +use serde::{Deserialize, Serialize}; + +use crate::clustering::ClusterAlgorithm; + +#[derive(Debug, Clone, Default, PartialEq, Serialize, Deserialize)] +#[serde(default)] +pub(crate) struct AnalyzeConfig { + pub(crate) analysis: AnalysisConfig, +} + +impl AnalyzeConfig { + pub(crate) fn load(project_root: &Path, explicit_path: Option<&Path>) -> Result { + if let Some(path) = explicit_path { + return Self::from_path(path) + .with_context(|| format!("load analyze config {}", path.display())); + } + + let default_path = project_root.join("clarion.yaml"); + if default_path.exists() { + Self::from_path(&default_path) + .with_context(|| format!("load analyze config {}", default_path.display())) + } else { + Ok(Self::default()) + } + } + + pub(crate) fn to_json_string(&self) -> Result { + serde_json::to_string(self).context("serialize resolved analyze config") + } + + fn from_path(path: &Path) -> Result { + let raw = fs::read_to_string(path) + .with_context(|| format!("read analyze config {}", path.display()))?; + Self::from_yaml_str(&raw) + } + + fn from_yaml_str(raw: &str) -> Result { + if raw.trim().is_empty() { + return Ok(Self::default()); + } + let config: Self = serde_norway::from_str(raw) + .map_err(|err| anyhow::anyhow!("invalid analyze config: {err}"))?; + config.validate()?; + Ok(config) + } + + fn validate(&self) -> Result<()> { + let clustering = &self.analysis.clustering; + ensure!( + clustering.resolution.is_finite() && clustering.resolution > 0.0, + "invalid analyze config: analysis.clustering.resolution must be a positive finite number" + ); + ensure!( + clustering.max_iterations > 0, + "invalid analyze config: analysis.clustering.max_iterations must be greater than zero" + ); + ensure!( + clustering.min_cluster_size > 0, + "invalid analyze config: analysis.clustering.min_cluster_size must be greater than zero" + ); + ensure!( + clustering.weak_modularity_threshold.is_finite() + && clustering.weak_modularity_threshold >= 0.0, + "invalid analyze config: analysis.clustering.weak_modularity_threshold must be a non-negative finite number" + ); + if clustering.edge_types.is_empty() { + bail!("invalid analyze config: analysis.clustering.edge_types must not be empty"); + } + Ok(()) + } +} + +#[derive(Debug, Clone, Default, PartialEq, Serialize, Deserialize)] +#[serde(default)] +pub(crate) struct AnalysisConfig { + pub(crate) clustering: ClusteringConfig, +} + +#[derive(Debug, Clone, PartialEq, Serialize, Deserialize)] +#[serde(default)] +pub(crate) struct ClusteringConfig { + pub(crate) enabled: bool, + pub(crate) algorithm: ClusterAlgorithm, + pub(crate) seed: u64, + pub(crate) resolution: f64, + pub(crate) max_iterations: u32, + pub(crate) min_cluster_size: usize, + pub(crate) edge_types: Vec, + pub(crate) weight_by: ClusteringWeightBy, + pub(crate) weak_modularity_threshold: f64, +} + +impl Default for ClusteringConfig { + fn default() -> Self { + Self { + enabled: true, + algorithm: ClusterAlgorithm::Leiden, + seed: 42, + resolution: 1.0, + max_iterations: 100, + min_cluster_size: 3, + edge_types: vec![ClusteringEdgeType::Imports, ClusteringEdgeType::Calls], + weight_by: ClusteringWeightBy::ReferenceCount, + weak_modularity_threshold: 0.3, + } + } +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "snake_case")] +pub(crate) enum ClusteringEdgeType { + Imports, + Calls, +} + +impl ClusteringEdgeType { + pub(crate) fn as_str(self) -> &'static str { + match self { + ClusteringEdgeType::Imports => "imports", + ClusteringEdgeType::Calls => "calls", + } + } +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)] +#[serde(rename_all = "snake_case")] +pub(crate) enum ClusteringWeightBy { + ReferenceCount, +} + +impl ClusteringWeightBy { + pub(crate) fn as_str(self) -> &'static str { + match self { + ClusteringWeightBy::ReferenceCount => "reference_count", + } + } +} diff --git a/crates/clarion-cli/src/install.rs b/crates/clarion-cli/src/install.rs index edfee0b5..a0d83b36 100644 --- a/crates/clarion-cli/src/install.rs +++ b/crates/clarion-cli/src/install.rs @@ -7,9 +7,7 @@ //! - `/clarion.yaml` (user-edited config stub at project root; //! see detailed-design.md §File layout) //! -//! Refuses if `.clarion/` already exists (UQ-WP1-08). `--force` is accepted -//! by the CLI but currently returns an error — Sprint 1 does not implement -//! overwrite. +//! Refuses if `.clarion/` already exists unless `--force` is passed. use std::fs; use std::path::Path; @@ -80,17 +78,10 @@ runs/*/log.jsonl /// /// # Errors /// -/// Returns an error if `--force` is passed (not implemented in Sprint 1), -/// if `.clarion/` already exists, if the target directory cannot be -/// canonicalised, or if any filesystem or database operation fails. +/// Returns an error if `.clarion/` already exists without `--force`, if the +/// target directory cannot be canonicalised, or if any filesystem or database +/// operation fails. pub fn run(path: &Path, force: bool) -> Result<()> { - if force { - bail!( - "--force is not implemented in Sprint 1. Remove .clarion/ manually \ - if you need a clean reinit." - ); - } - if !path.exists() { bail!( "target directory does not exist: {}. Create it first or pass a valid --path.", @@ -102,11 +93,21 @@ pub fn run(path: &Path, force: bool) -> Result<()> { .with_context(|| format!("cannot canonicalise --path {}", path.display()))?; let clarion_dir = project_root.join(".clarion"); if clarion_dir.exists() { - bail!( - ".clarion/ already exists at {}. Delete it (or pass --force when \ - Sprint 2+ implements overwrite) and try again.", - clarion_dir.display() - ); + if !force { + bail!( + ".clarion/ already exists at {}. Delete it or pass --force to overwrite it.", + clarion_dir.display() + ); + } + if !clarion_dir.is_dir() { + bail!( + "--force can only overwrite an existing .clarion/ directory; \ + found non-directory at {}.", + clarion_dir.display() + ); + } + fs::remove_dir_all(&clarion_dir) + .with_context(|| format!("remove existing {}", clarion_dir.display()))?; } fs::create_dir_all(&clarion_dir).with_context(|| format!("mkdir {}", clarion_dir.display()))?; diff --git a/crates/clarion-cli/src/main.rs b/crates/clarion-cli/src/main.rs index fa557a3b..048d96c5 100644 --- a/crates/clarion-cli/src/main.rs +++ b/crates/clarion-cli/src/main.rs @@ -1,5 +1,7 @@ mod analyze; mod cli; +mod clustering; +mod config; mod install; mod serve; mod stats; @@ -8,15 +10,30 @@ use anyhow::Result; use clap::Parser; fn main() -> Result<()> { + // Load .env from CWD or any ancestor directory, before tracing setup so a + // .env-supplied RUST_LOG is in effect by the time the filter is built. + // Existing process env vars win over .env values (dotenvy default), so an + // explicit `OPENROUTER_API_KEY=… clarion serve` still beats a checked-in + // dev .env. Missing .env is not an error — silently skip. + let _ = dotenvy::dotenv(); init_tracing(); let cli = cli::Cli::parse(); match cli.command { cli::Command::Install { force, path } => install::run(&path, force), - cli::Command::Analyze { path } => { + cli::Command::Analyze { path, config } => { let rt = tokio::runtime::Builder::new_multi_thread() .enable_all() .build()?; - rt.block_on(analyze::run(path)) + if let Some(config_path) = config { + rt.block_on(analyze::run_with_options( + path, + analyze::AnalyzeOptions { + config_path: Some(config_path), + }, + )) + } else { + rt.block_on(analyze::run(path)) + } } cli::Command::Serve { path, config } => serve::run(&path, config.as_deref()), } diff --git a/crates/clarion-cli/tests/analyze.rs b/crates/clarion-cli/tests/analyze.rs index 65309292..f72b910e 100644 --- a/crates/clarion-cli/tests/analyze.rs +++ b/crates/clarion-cli/tests/analyze.rs @@ -7,6 +7,30 @@ fn clarion_bin() -> Command { Command::cargo_bin("clarion").expect("clarion binary") } +fn latest_run_config(project_root: &std::path::Path) -> serde_json::Value { + let conn = Connection::open(project_root.join(".clarion/clarion.db")).unwrap(); + let config_raw: String = conn + .query_row( + "SELECT config FROM runs ORDER BY started_at DESC LIMIT 1", + [], + |row| row.get(0), + ) + .expect("query latest runs.config"); + serde_json::from_str(&config_raw).expect("runs.config JSON") +} + +fn latest_run_stats(project_root: &std::path::Path) -> serde_json::Value { + let conn = Connection::open(project_root.join(".clarion/clarion.db")).unwrap(); + let stats_raw: String = conn + .query_row( + "SELECT stats FROM runs ORDER BY started_at DESC LIMIT 1", + [], + |row| row.get(0), + ) + .expect("query latest runs.stats"); + serde_json::from_str(&stats_raw).expect("runs.stats JSON") +} + #[cfg(unix)] const AMBIGUOUS_CALLS_PLUGIN_SCRIPT: &str = r#"#!/usr/bin/python3 import json @@ -124,6 +148,8 @@ while True: "references_skipped_cap_total": 6, "unresolved_reference_sites_total": 7, "pyright_query_latency_ms": list(range(10, 1010, 10)), + "pyright_index_parse_latency_ms": [4, 8, 12], + "extractor_parse_latency_ms": 6, }, }, }) @@ -157,6 +183,239 @@ rule_id_prefix = "CLA-CALLS-" ontology_version = "0.4.0" "#; +#[cfg(unix)] +const IMPORTS_PLUGIN_SCRIPT: &str = r#"#!/usr/bin/python3 +import json +import pathlib +import sys + + +def read_frame(): + headers = {} + while True: + line = sys.stdin.buffer.readline() + if line in (b"", b"\r\n"): + break + name, value = line.decode("ascii").strip().split(":", 1) + headers[name.lower()] = value.strip() + length = int(headers["content-length"]) + return json.loads(sys.stdin.buffer.read(length)) + + +def write_frame(message): + body = json.dumps(message, separators=(",", ":")).encode("utf-8") + sys.stdout.buffer.write(b"Content-Length: " + str(len(body)).encode("ascii") + b"\r\n\r\n") + sys.stdout.buffer.write(body) + sys.stdout.buffer.flush() + + +while True: + msg = read_frame() + method = msg.get("method") + if method == "initialized": + continue + if method == "exit": + raise SystemExit(0) + ident = msg["id"] + if method == "initialize": + write_frame({ + "jsonrpc": "2.0", + "id": ident, + "result": { + "name": "clarion-plugin-imports", + "version": "0.1.0", + "ontology_version": "0.6.0", + "capabilities": {}, + }, + }) + elif method == "analyze_file": + path = msg["params"]["file_path"] + stem = pathlib.Path(path).stem + module_id = f"importsfixture:module:{stem}" + edges = [] + if stem == "consumer": + edges = [ + { + "kind": "imports", + "from_id": module_id, + "to_id": "importsfixture:module:internal", + "source_byte_start": 0, + "source_byte_end": 15, + "confidence": "resolved", + "properties": {"imported_name": "internal"}, + }, + { + "kind": "imports", + "from_id": module_id, + "to_id": "importsfixture:module:external", + "source_byte_start": 16, + "source_byte_end": 31, + "confidence": "resolved", + "properties": {"imported_name": "external"}, + }, + ] + write_frame({ + "jsonrpc": "2.0", + "id": ident, + "result": { + "entities": [ + { + "id": module_id, + "kind": "module", + "qualified_name": stem, + "source": {"file_path": path}, + }, + ], + "edges": edges, + "stats": {}, + }, + }) + elif method == "shutdown": + write_frame({"jsonrpc": "2.0", "id": ident, "result": {}}) + else: + raise SystemExit(1) +"#; + +#[cfg(unix)] +const IMPORTS_PLUGIN_MANIFEST: &str = r#" +[plugin] +name = "clarion-plugin-imports" +plugin_id = "importsfixture" +version = "0.1.0" +protocol_version = "1.0" +executable = "clarion-plugin-imports" +language = "importsfixture" +extensions = ["imp"] + +[capabilities.runtime] +expected_max_rss_mb = 256 +expected_entities_per_file = 100 +wardline_aware = false +reads_outside_project_root = false + +[ontology] +entity_kinds = ["module"] +edge_kinds = ["imports"] +rule_id_prefix = "CLA-IMPORTS-" +ontology_version = "0.6.0" +"#; + +#[cfg(unix)] +const PHASE3_PLUGIN_SCRIPT: &str = r#"#!/usr/bin/python3 +import json +import pathlib +import sys + + +def read_frame(): + headers = {} + while True: + line = sys.stdin.buffer.readline() + if line in (b"", b"\r\n"): + break + name, value = line.decode("ascii").strip().split(":", 1) + headers[name.lower()] = value.strip() + length = int(headers["content-length"]) + return json.loads(sys.stdin.buffer.read(length)) + + +def write_frame(message): + body = json.dumps(message, separators=(",", ":")).encode("utf-8") + sys.stdout.buffer.write(b"Content-Length: " + str(len(body)).encode("ascii") + b"\r\n\r\n") + sys.stdout.buffer.write(body) + sys.stdout.buffer.flush() + + +TARGETS = { + "auth_a": ["auth_b"], + "auth_b": ["auth_a"], + "billing_a": ["billing_b"], + "billing_b": ["billing_a"], + "weak_a": ["weak_b"], +} + + +while True: + msg = read_frame() + method = msg.get("method") + if method == "initialized": + continue + if method == "exit": + raise SystemExit(0) + ident = msg["id"] + if method == "initialize": + write_frame({ + "jsonrpc": "2.0", + "id": ident, + "result": { + "name": "clarion-plugin-phase3", + "version": "0.1.0", + "ontology_version": "0.6.0", + "capabilities": {}, + }, + }) + elif method == "analyze_file": + path = msg["params"]["file_path"] + stem = pathlib.Path(path).stem + module_id = f"phase3fixture:module:{stem}" + edges = [ + { + "kind": "imports", + "from_id": module_id, + "to_id": f"phase3fixture:module:{target}", + "source_byte_start": 0, + "source_byte_end": 10, + "confidence": "resolved", + "properties": {"imported_name": target}, + } + for target in TARGETS.get(stem, []) + ] + write_frame({ + "jsonrpc": "2.0", + "id": ident, + "result": { + "entities": [ + { + "id": module_id, + "kind": "module", + "qualified_name": stem, + "source": {"file_path": path}, + }, + ], + "edges": edges, + "stats": {}, + }, + }) + elif method == "shutdown": + write_frame({"jsonrpc": "2.0", "id": ident, "result": {}}) + else: + raise SystemExit(1) +"#; + +#[cfg(unix)] +const PHASE3_PLUGIN_MANIFEST: &str = r#" +[plugin] +name = "clarion-plugin-phase3" +plugin_id = "phase3fixture" +version = "0.1.0" +protocol_version = "1.0" +executable = "clarion-plugin-phase3" +language = "phase3fixture" +extensions = ["p3"] + +[capabilities.runtime] +expected_max_rss_mb = 256 +expected_entities_per_file = 100 +wardline_aware = false +reads_outside_project_root = false + +[ontology] +entity_kinds = ["module"] +edge_kinds = ["imports"] +rule_id_prefix = "CLA-PHASE3-" +ontology_version = "0.6.0" +"#; + #[cfg(unix)] fn write_ambiguous_calls_plugin(plugin_dir: &std::path::Path) { use std::os::unix::fs::PermissionsExt; @@ -177,6 +436,92 @@ fn write_ambiguous_calls_plugin(plugin_dir: &std::path::Path) { .expect("write calls plugin manifest"); } +#[cfg(unix)] +fn write_imports_plugin(plugin_dir: &std::path::Path) { + use std::os::unix::fs::PermissionsExt; + + let plugin_script = plugin_dir.join("clarion-plugin-imports"); + std::fs::write(&plugin_script, IMPORTS_PLUGIN_SCRIPT).expect("write imports plugin script"); + let mut perms = std::fs::metadata(&plugin_script) + .expect("stat imports plugin") + .permissions(); + perms.set_mode(0o755); + std::fs::set_permissions(&plugin_script, perms).expect("chmod imports plugin"); + + std::fs::write(plugin_dir.join("plugin.toml"), IMPORTS_PLUGIN_MANIFEST) + .expect("write imports plugin manifest"); +} + +#[cfg(unix)] +fn write_phase3_plugin(plugin_dir: &std::path::Path) { + use std::os::unix::fs::PermissionsExt; + + let plugin_script = plugin_dir.join("clarion-plugin-phase3"); + std::fs::write(&plugin_script, PHASE3_PLUGIN_SCRIPT).expect("write phase3 plugin script"); + let mut perms = std::fs::metadata(&plugin_script) + .expect("stat phase3 plugin") + .permissions(); + perms.set_mode(0o755); + std::fs::set_permissions(&plugin_script, perms).expect("chmod phase3 plugin"); + + std::fs::write(plugin_dir.join("plugin.toml"), PHASE3_PLUGIN_MANIFEST) + .expect("write phase3 plugin manifest"); +} + +#[cfg(unix)] +fn run_phase3_fixture(stems: &[&str], config_yaml: &str) -> tempfile::TempDir { + let project_dir = tempfile::tempdir().unwrap(); + let plugin_dir = tempfile::tempdir().unwrap(); + write_phase3_plugin(plugin_dir.path()); + + clarion_bin() + .args(["install", "--path"]) + .arg(project_dir.path()) + .assert() + .success(); + for stem in stems { + std::fs::write(project_dir.path().join(format!("{stem}.p3")), b"module\n") + .expect("write phase3 fixture file"); + } + let config_path = project_dir.path().join("phase3-clarion.yaml"); + std::fs::write(&config_path, config_yaml).expect("write phase3 config"); + + let plugin_path = + std::env::join_paths(std::iter::once(plugin_dir.path().to_path_buf())).unwrap(); + clarion_bin() + .args(["analyze", "--config"]) + .arg(&config_path) + .arg(project_dir.path()) + .env("PATH", &plugin_path) + .assert() + .success(); + + project_dir +} + +#[cfg(unix)] +fn phase3_config(min_cluster_size: u64) -> String { + format!( + r" +analysis: + clustering: + min_cluster_size: {min_cluster_size} +" + ) +} + +#[cfg(unix)] +fn phase3_weighted_components_config(min_cluster_size: u64) -> String { + format!( + r" +analysis: + clustering: + algorithm: weighted_components + min_cluster_size: {min_cluster_size} +" + ) +} + #[test] fn analyze_without_plugins_writes_skipped_run_row() { let dir = tempfile::tempdir().unwrap(); @@ -217,6 +562,386 @@ fn analyze_without_plugins_writes_skipped_run_row() { assert_eq!(entity_count, 0); } +#[test] +fn analyze_default_config_records_clustering_defaults() { + let dir = tempfile::tempdir().unwrap(); + + clarion_bin() + .args(["install", "--path"]) + .arg(dir.path()) + .env("PATH", "") + .assert() + .success(); + + clarion_bin() + .args(["analyze"]) + .arg(dir.path()) + .env("PATH", "") + .assert() + .success(); + + let config = latest_run_config(dir.path()); + let clustering = &config["analysis"]["clustering"]; + assert_eq!(clustering["enabled"].as_bool(), Some(true)); + assert_eq!(clustering["algorithm"].as_str(), Some("leiden")); + assert_eq!(clustering["seed"].as_u64(), Some(42)); + assert_eq!(clustering["resolution"].as_f64(), Some(1.0)); + assert_eq!(clustering["max_iterations"].as_u64(), Some(100)); + assert_eq!(clustering["min_cluster_size"].as_u64(), Some(3)); + assert_eq!( + clustering["edge_types"], + serde_json::json!(["imports", "calls"]) + ); + assert_eq!(clustering["weight_by"].as_str(), Some("reference_count")); + assert_eq!(clustering["weak_modularity_threshold"].as_f64(), Some(0.3)); +} + +#[test] +fn analyze_config_file_overrides_clustering_seed_and_algorithm() { + let dir = tempfile::tempdir().unwrap(); + + clarion_bin() + .args(["install", "--path"]) + .arg(dir.path()) + .env("PATH", "") + .assert() + .success(); + let config_path = dir.path().join("custom-clarion.yaml"); + std::fs::write( + &config_path, + r" +analysis: + clustering: + algorithm: weighted_components + seed: 99 + weak_modularity_threshold: 0.0 +", + ) + .expect("write analyze config"); + + clarion_bin() + .args(["analyze", "--config"]) + .arg(&config_path) + .arg(dir.path()) + .env("PATH", "") + .assert() + .success(); + + let config = latest_run_config(dir.path()); + let clustering = &config["analysis"]["clustering"]; + assert_eq!( + clustering["algorithm"].as_str(), + Some("weighted_components") + ); + assert_eq!(clustering["seed"].as_u64(), Some(99)); + assert_eq!(clustering["enabled"].as_bool(), Some(true)); + assert_eq!(clustering["max_iterations"].as_u64(), Some(100)); + assert_eq!(clustering["weak_modularity_threshold"].as_f64(), Some(0.0)); +} + +#[test] +fn analyze_rejects_invalid_clustering_algorithm() { + let dir = tempfile::tempdir().unwrap(); + + clarion_bin() + .args(["install", "--path"]) + .arg(dir.path()) + .env("PATH", "") + .assert() + .success(); + let config_path = dir.path().join("bad-clarion.yaml"); + std::fs::write( + &config_path, + r" +analysis: + clustering: + algorithm: spectral +", + ) + .expect("write invalid analyze config"); + + let out = clarion_bin() + .args(["analyze", "--config"]) + .arg(&config_path) + .arg(dir.path()) + .env("PATH", "") + .assert() + .failure(); + let stderr = String::from_utf8(out.get_output().stderr.clone()).unwrap(); + assert!( + stderr.contains("invalid analyze config") && stderr.contains("algorithm"), + "stderr should identify invalid clustering algorithm; got: {stderr}" + ); + + let conn = Connection::open(dir.path().join(".clarion/clarion.db")).unwrap(); + let run_count: i64 = conn + .query_row("SELECT COUNT(*) FROM runs", [], |row| row.get(0)) + .expect("query run count"); + assert_eq!(run_count, 0, "invalid config must fail before BeginRun"); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_emits_subsystem_entities_and_edges() { + let project_dir = run_phase3_fixture( + &["auth_a", "auth_b", "billing_a", "billing_b"], + &phase3_config(2), + ); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + + let subsystem_count: i64 = conn + .query_row( + "SELECT COUNT(*) FROM entities WHERE kind = 'subsystem'", + [], + |row| row.get(0), + ) + .expect("query subsystem count"); + assert!( + subsystem_count >= 2, + "expected at least two subsystem entities, got {subsystem_count}" + ); + + let in_subsystem_edges: i64 = conn + .query_row( + "SELECT COUNT(*) FROM edges WHERE kind = 'in_subsystem'", + [], + |row| row.get(0), + ) + .expect("query in_subsystem edge count"); + assert_eq!(in_subsystem_edges, 4); + + let stats = latest_run_stats(project_dir.path()); + let clustering = &stats["clustering"]; + assert_eq!(clustering["status"].as_str(), Some("completed")); + assert_eq!(clustering["subsystems_inserted"].as_u64(), Some(2)); + assert_eq!(clustering["in_subsystem_edges_inserted"].as_u64(), Some(4)); + assert_eq!(clustering["module_count"].as_u64(), Some(4)); + assert_eq!(clustering["module_edge_count"].as_u64(), Some(4)); + assert_eq!(clustering["configured_algorithm"].as_str(), Some("leiden")); + assert_eq!( + clustering["algorithm"].as_str(), + Some("weighted_components") + ); + assert!(clustering["modularity_score"].is_number()); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_is_deterministic_across_two_runs() { + fn signature(project_root: &std::path::Path) -> Vec<(String, String)> { + let conn = Connection::open(project_root.join(".clarion/clarion.db")).unwrap(); + conn.prepare("SELECT id, properties FROM entities WHERE kind = 'subsystem' ORDER BY id") + .unwrap() + .query_map([], |row| Ok((row.get(0)?, row.get(1)?))) + .unwrap() + .collect::>() + .unwrap() + } + + let config = phase3_config(2); + let first = run_phase3_fixture(&["auth_a", "auth_b", "billing_a", "billing_b"], &config); + let second = run_phase3_fixture(&["auth_a", "auth_b", "billing_a", "billing_b"], &config); + + assert_eq!(signature(first.path()), signature(second.path())); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_skips_empty_graph_with_stats() { + let project_dir = run_phase3_fixture(&["solo"], &phase3_config(2)); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let subsystem_count: i64 = conn + .query_row( + "SELECT COUNT(*) FROM entities WHERE kind = 'subsystem'", + [], + |row| row.get(0), + ) + .expect("query subsystem count"); + assert_eq!(subsystem_count, 0); + + let stats = latest_run_stats(project_dir.path()); + let clustering = &stats["clustering"]; + assert_eq!(clustering["status"].as_str(), Some("skipped")); + assert_eq!( + clustering["skipped_reason"].as_str(), + Some("no_module_dependency_edges") + ); + assert_eq!(clustering["module_count"].as_u64(), Some(1)); + assert_eq!(clustering["module_edge_count"].as_u64(), Some(0)); + assert_eq!(clustering["subsystems_inserted"].as_u64(), Some(0)); + assert_eq!(clustering["in_subsystem_edges_inserted"].as_u64(), Some(0)); + assert!(clustering["modularity_score"].is_null()); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_emits_weak_modularity_fact_when_below_threshold() { + let project_dir = run_phase3_fixture(&["weak_a", "weak_b"], &phase3_config(2)); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let row: (String, String, String, String, String) = conn + .query_row( + "SELECT rule_id, kind, severity, status, properties \ + FROM findings WHERE rule_id = 'CLA-FACT-CLUSTERING-WEAK-MODULARITY'", + [], + |row| { + Ok(( + row.get(0)?, + row.get(1)?, + row.get(2)?, + row.get(3)?, + row.get(4)?, + )) + }, + ) + .expect("query weak modularity finding"); + assert_eq!(row.0, "CLA-FACT-CLUSTERING-WEAK-MODULARITY"); + assert_eq!(row.1, "fact"); + assert_eq!(row.2, "INFO"); + assert_eq!(row.3, "open"); + let properties: serde_json::Value = serde_json::from_str(&row.4).expect("finding properties"); + assert_eq!(properties["threshold"].as_f64(), Some(0.3)); + assert_eq!(properties["algorithm"].as_str(), Some("leiden")); + assert!(properties["modularity_score"].as_f64().unwrap_or(1.0) < 0.3); + + let stats = latest_run_stats(project_dir.path()); + assert_eq!( + stats["clustering"]["weak_modularity_finding_emitted"].as_bool(), + Some(true) + ); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_weak_modularity_threshold_zero_disables_fact() { + let project_dir = run_phase3_fixture( + &["weak_a", "weak_b"], + r" +analysis: + clustering: + min_cluster_size: 2 + weak_modularity_threshold: 0.0 +", + ); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let finding_count: i64 = conn + .query_row( + "SELECT COUNT(*) FROM findings \ + WHERE rule_id = 'CLA-FACT-CLUSTERING-WEAK-MODULARITY'", + [], + |row| row.get(0), + ) + .expect("query weak modularity finding count"); + assert_eq!(finding_count, 0); + + let stats = latest_run_stats(project_dir.path()); + assert_eq!( + stats["clustering"]["weak_modularity_threshold"].as_f64(), + Some(0.0) + ); + assert_eq!( + stats["clustering"]["weak_modularity_finding_emitted"].as_bool(), + Some(false) + ); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_does_not_emit_weak_modularity_fact_when_threshold_is_met() { + let project_dir = run_phase3_fixture( + &["auth_a", "auth_b", "billing_a", "billing_b"], + &phase3_config(2), + ); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let finding_count: i64 = conn + .query_row( + "SELECT COUNT(*) FROM findings \ + WHERE rule_id = 'CLA-FACT-CLUSTERING-WEAK-MODULARITY'", + [], + |row| row.get(0), + ) + .expect("query weak modularity finding count"); + assert_eq!(finding_count, 0); + + let stats = latest_run_stats(project_dir.path()); + assert_eq!( + stats["clustering"]["weak_modularity_finding_emitted"].as_bool(), + Some(false) + ); + assert!( + stats["clustering"]["modularity_score"] + .as_f64() + .unwrap_or_default() + >= 0.3 + ); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_min_cluster_size_drops_undersized_weighted_components() { + let project_dir = run_phase3_fixture( + &["auth_a", "auth_b", "billing_a", "billing_b"], + &phase3_weighted_components_config(3), + ); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let subsystem_count: i64 = conn + .query_row( + "SELECT COUNT(*) FROM entities WHERE kind = 'subsystem'", + [], + |row| row.get(0), + ) + .expect("query subsystem count"); + assert_eq!(subsystem_count, 0); + + let in_subsystem_edges: i64 = conn + .query_row( + "SELECT COUNT(*) FROM edges WHERE kind = 'in_subsystem'", + [], + |row| row.get(0), + ) + .expect("query in_subsystem edge count"); + assert_eq!(in_subsystem_edges, 0); + + let stats = latest_run_stats(project_dir.path()); + let clustering = &stats["clustering"]; + assert_eq!(clustering["status"].as_str(), Some("skipped")); + assert_eq!( + clustering["skipped_reason"].as_str(), + Some("no_clusters_emitted") + ); + assert_eq!(clustering["subsystems_inserted"].as_u64(), Some(0)); + assert_eq!(clustering["in_subsystem_edges_inserted"].as_u64(), Some(0)); +} + +#[cfg(unix)] +#[test] +fn analyze_phase3_persists_weighted_components_algorithm_when_selected() { + let project_dir = run_phase3_fixture( + &["auth_a", "auth_b", "billing_a", "billing_b"], + &phase3_weighted_components_config(2), + ); + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let properties_json: String = conn + .query_row( + "SELECT properties FROM entities \ + WHERE kind = 'subsystem' ORDER BY id LIMIT 1", + [], + |row| row.get(0), + ) + .expect("query subsystem properties"); + let properties: serde_json::Value = + serde_json::from_str(&properties_json).expect("subsystem properties JSON"); + assert_eq!( + properties["algorithm"].as_str(), + Some("weighted_components") + ); + + let stats = latest_run_stats(project_dir.path()); + assert_eq!( + stats["clustering"]["algorithm"].as_str(), + Some("weighted_components") + ); +} + #[test] fn analyze_fails_cleanly_if_clarion_dir_missing() { let dir = tempfile::tempdir().unwrap(); @@ -300,6 +1025,16 @@ fn analyze_stats_reports_ambiguous_edges_total() { Some(950), "pyright_query_latency_p95_ms should be the deterministic p95; got {stats_raw}" ); + assert_eq!( + stats["pyright_index_parse_latency_p95_ms"].as_u64(), + Some(12), + "pyright_index_parse_latency_p95_ms should be aggregated; got {stats_raw}" + ); + assert_eq!( + stats["extractor_parse_latency_p95_ms"].as_u64(), + Some(6), + "extractor_parse_latency_p95_ms should be aggregated; got {stats_raw}" + ); let unresolved_row: (String, String, i64, i64) = conn .query_row( "SELECT caller_entity_id, callee_expr, source_byte_start, source_byte_end \ @@ -319,6 +1054,62 @@ fn analyze_stats_reports_ambiguous_edges_total() { ); } +#[cfg(unix)] +#[test] +fn analyze_filters_external_import_edges_before_writer_insert() { + let project_dir = tempfile::tempdir().unwrap(); + let plugin_dir = tempfile::tempdir().unwrap(); + write_imports_plugin(plugin_dir.path()); + + clarion_bin() + .args(["install", "--path"]) + .arg(project_dir.path()) + .assert() + .success(); + std::fs::write( + project_dir.path().join("consumer.imp"), + b"import internal\n", + ) + .expect("write consumer.imp"); + std::fs::write(project_dir.path().join("internal.imp"), b"# internal\n") + .expect("write internal.imp"); + + let plugin_path = + std::env::join_paths(std::iter::once(plugin_dir.path().to_path_buf())).unwrap(); + clarion_bin() + .args(["analyze"]) + .arg(project_dir.path()) + .env("PATH", &plugin_path) + .assert() + .success(); + + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let import_edges: Vec<(String, String)> = conn + .prepare("SELECT from_id, to_id FROM edges WHERE kind = 'imports' ORDER BY from_id, to_id") + .unwrap() + .query_map([], |row| Ok((row.get(0)?, row.get(1)?))) + .unwrap() + .collect::>() + .unwrap(); + assert_eq!( + import_edges, + vec![( + "importsfixture:module:consumer".to_owned(), + "importsfixture:module:internal".to_owned(), + )], + ); + + let stats_raw: String = conn + .query_row("SELECT stats FROM runs LIMIT 1", [], |row| row.get(0)) + .expect("query runs.stats"); + let stats: serde_json::Value = serde_json::from_str(&stats_raw).expect("stats JSON"); + assert_eq!( + stats["imports_skipped_external_total"].as_u64(), + Some(1), + "host should count the filtered external import; got {stats_raw}" + ); +} + /// Regression for wp2 review-2 (clarion-f56dc6ee43): `FailRun` must exit /// non-zero so `clarion analyze && next` chains and CI gating work. /// diff --git a/crates/clarion-cli/tests/install.rs b/crates/clarion-cli/tests/install.rs index ce79b5cd..e6a02d88 100644 --- a/crates/clarion-cli/tests/install.rs +++ b/crates/clarion-cli/tests/install.rs @@ -99,17 +99,36 @@ fn install_refuses_to_overwrite_existing_clarion_dir() { } #[test] -fn install_force_returns_unimplemented_in_sprint_one() { +fn install_force_replaces_existing_clarion_dir_without_overwriting_yaml() { let dir = tempfile::tempdir().unwrap(); - let out = clarion_bin() + clarion_bin() + .args(["install", "--path"]) + .arg(dir.path()) + .assert() + .success(); + + let clarion = dir.path().join(".clarion"); + fs::write(clarion.join("stale.tmp"), "stale").unwrap(); + fs::write( + dir.path().join("clarion.yaml"), + "version: 1\ncustom: true\n", + ) + .unwrap(); + + clarion_bin() .args(["install", "--force", "--path"]) .arg(dir.path()) .assert() - .failure(); - let stderr = String::from_utf8(out.get_output().stderr.clone()).unwrap(); + .success(); + assert!( - stderr.contains("not implemented in Sprint 1"), - "expected Sprint 1 --force stub message: {stderr}" + !clarion.join("stale.tmp").exists(), + "--force should remove stale .clarion/ contents" + ); + assert!(clarion.join("clarion.db").exists(), "clarion.db missing"); + assert_eq!( + fs::read_to_string(dir.path().join("clarion.yaml")).unwrap(), + "version: 1\ncustom: true\n" ); } @@ -169,3 +188,79 @@ fn install_leaves_existing_clarion_yaml_untouched() { "clarion.yaml was overwritten; user content lost" ); } + +#[test] +fn dotenv_in_cwd_is_loaded_before_tracing_setup() { + // Proves the dotenvy hook in `main()` runs before `init_tracing()`: a + // `.env`-supplied RUST_LOG=debug enables the debug-level log line in + // `install` (the "clarion.yaml already exists; leaving untouched" + // branch in install.rs) that the default `info` filter would + // otherwise suppress. Pre-creating `clarion.yaml` puts us on the + // branch that emits debug. + // + // Uses raw std::process::Command rather than assert_cmd::Command so the + // child env is exactly what we set — assert_cmd's wrappers were observed + // to drop the env_remove/env_clear effect on RUST_LOG under nextest, + // producing an empty stderr regardless of .env content. + let dir = tempfile::tempdir().unwrap(); + fs::write(dir.path().join(".env"), "RUST_LOG=debug\n").unwrap(); + fs::write(dir.path().join("clarion.yaml"), "version: 1\n").unwrap(); + + let bin = assert_cmd::cargo::cargo_bin("clarion"); + let path = std::env::var("PATH").unwrap_or_default(); + let out = std::process::Command::new(&bin) + .current_dir(dir.path()) + .env_clear() + .env("PATH", path) + .args(["install", "--path"]) + .arg(dir.path()) + .output() + .expect("clarion install"); + + let stdout = String::from_utf8_lossy(&out.stdout); + let stderr = String::from_utf8_lossy(&out.stderr); + assert!( + out.status.success(), + "install failed; stdout:\n{stdout}\nstderr:\n{stderr}" + ); + // tracing_subscriber::fmt defaults to stdout, so the DEBUG line lands there. + assert!( + stdout.contains("DEBUG"), + ".env-supplied RUST_LOG=debug should produce DEBUG-level lines on stdout; \ + stdout was:\n{stdout}" + ); +} + +#[test] +fn explicit_env_var_wins_over_dotenv() { + // dotenvy's default semantics: existing process env vars are NOT clobbered + // by .env entries. An explicit `RUST_LOG=info` in the process env should + // suppress the debug line even when .env tries to bump verbosity. + let dir = tempfile::tempdir().unwrap(); + fs::write(dir.path().join(".env"), "RUST_LOG=debug\n").unwrap(); + fs::write(dir.path().join("clarion.yaml"), "version: 1\n").unwrap(); + + let bin = assert_cmd::cargo::cargo_bin("clarion"); + let path = std::env::var("PATH").unwrap_or_default(); + let out = std::process::Command::new(&bin) + .current_dir(dir.path()) + .env_clear() + .env("PATH", path) + .env("RUST_LOG", "info") + .args(["install", "--path"]) + .arg(dir.path()) + .output() + .expect("clarion install"); + + let stdout = String::from_utf8_lossy(&out.stdout); + let stderr = String::from_utf8_lossy(&out.stderr); + assert!( + out.status.success(), + "install failed; stdout:\n{stdout}\nstderr:\n{stderr}" + ); + assert!( + !stdout.contains("DEBUG"), + "explicit RUST_LOG=info should beat .env's RUST_LOG=debug; \ + stdout was:\n{stdout}" + ); +} diff --git a/crates/clarion-cli/tests/wp2_e2e.rs b/crates/clarion-cli/tests/wp2_e2e.rs index cbc13b46..1b3fa1ad 100644 --- a/crates/clarion-cli/tests/wp2_e2e.rs +++ b/crates/clarion-cli/tests/wp2_e2e.rs @@ -20,6 +20,7 @@ use std::path::PathBuf; use std::{env, fs}; use assert_cmd::Command; +use clarion_core::plugin::limits::FINDING_OOM_KILLED; use rusqlite::Connection; use tempfile::TempDir; @@ -96,6 +97,40 @@ fn setup_plugin_dir(fixture_bin: &PathBuf) -> TempDir { plugin_dir } +#[cfg(target_os = "linux")] +fn setup_oom_plugin_dir(fixture_bin: &PathBuf) -> TempDir { + let plugin_dir = TempDir::new().expect("create oom plugin tempdir"); + + let dest = plugin_dir.path().join("clarion-plugin-oom"); + std::os::unix::fs::symlink(fixture_bin, &dest).expect("symlink clarion-plugin-oom"); + + let manifest = r#" +[plugin] +name = "clarion-plugin-oom" +plugin_id = "oom" +version = "0.1.0" +protocol_version = "1.0" +executable = "clarion-plugin-oom" +language = "fixture" +extensions = ["oom"] + +[capabilities.runtime] +expected_max_rss_mb = 64 +expected_entities_per_file = 100 +wardline_aware = false +reads_outside_project_root = false + +[ontology] +entity_kinds = ["widget"] +edge_kinds = [] +rule_id_prefix = "CLA-OOM-" +ontology_version = "0.1.0" +"#; + fs::write(plugin_dir.path().join("plugin.toml"), manifest).expect("write oom plugin.toml"); + + plugin_dir +} + #[test] fn wp2_e2e_smoke_fixture_plugin_round_trip() { // 1. Locate the fixture binary. @@ -208,6 +243,55 @@ fn wp2_e2e_smoke_fixture_plugin_round_trip() { ); } +#[test] +#[cfg(target_os = "linux")] +fn wp2_rlimit_as_oom_kill_is_reported_as_host_finding() { + let fixture_bin = fixture_binary_path(); + let plugin_dir = setup_oom_plugin_dir(&fixture_bin); + + let project_dir = TempDir::new().expect("create project tempdir"); + clarion_bin() + .args(["install", "--path"]) + .arg(project_dir.path()) + .assert() + .success(); + fs::write(project_dir.path().join("demo.oom"), b"oom trigger\n").expect("write demo.oom"); + + let new_path = + env::join_paths(std::iter::once(plugin_dir.path().to_path_buf())).expect("join_paths"); + + let out = clarion_bin() + .args(["analyze"]) + .arg(project_dir.path()) + .env("PATH", &new_path) + .env("CLARION_FIXTURE_EXCEED_RLIMIT_AS", "1") + .assert() + .failure(); + let stdout = String::from_utf8(out.get_output().stdout.clone()).unwrap(); + let stderr = String::from_utf8(out.get_output().stderr.clone()).unwrap(); + assert!( + stdout.contains(FINDING_OOM_KILLED), + "OOM finding missing from analyze output.\nstdout: {stdout}\nstderr: {stderr}" + ); + + let conn = Connection::open(project_dir.path().join(".clarion/clarion.db")).unwrap(); + let (run_status, stats_raw): (String, String) = conn + .query_row("SELECT status, stats FROM runs LIMIT 1", [], |row| { + Ok((row.get(0)?, row.get(1)?)) + }) + .expect("query run row"); + assert_eq!(run_status, "failed"); + let stats: serde_json::Value = + serde_json::from_str(&stats_raw).expect("stats must be valid JSON"); + let failure_reason = stats["failure_reason"] + .as_str() + .expect("failure_reason must be a string"); + assert!( + failure_reason.contains("oom"), + "failure_reason should name the OOM plugin; got {failure_reason:?}" + ); +} + /// Regression for wp2 review-2 (clarion-978c8d6f15): crash-loop breaker is /// wired into the production analyze path AND a single plugin crash no /// longer tanks the whole run. diff --git a/crates/clarion-core/src/entity_id.rs b/crates/clarion-core/src/entity_id.rs index b5251c7c..3f47964f 100644 --- a/crates/clarion-core/src/entity_id.rs +++ b/crates/clarion-core/src/entity_id.rs @@ -128,26 +128,12 @@ fn validate_grammar(field: &'static str, value: &str) -> Result<(), EntityIdErro return Err(EntityIdError::EmptySegment { field }); } validate_no_colon(field, value)?; - let mut chars = value.chars(); - let Some(first) = chars.next() else { - // Unreachable: emptiness is checked above, but the defensive branch - // avoids any panic path and satisfies clippy::unwrap_in_result. - return Err(EntityIdError::EmptySegment { field }); - }; - if !first.is_ascii_lowercase() { + if !validate_kind_grammar(value) { return Err(EntityIdError::GrammarViolation { field, value: value.to_owned(), }); } - for c in chars { - if !(c.is_ascii_lowercase() || c.is_ascii_digit() || c == '_') { - return Err(EntityIdError::GrammarViolation { - field, - value: value.to_owned(), - }); - } - } Ok(()) } diff --git a/crates/clarion-core/src/llm_provider.rs b/crates/clarion-core/src/llm_provider.rs index c55ac53d..2ddfdeb5 100644 --- a/crates/clarion-core/src/llm_provider.rs +++ b/crates/clarion-core/src/llm_provider.rs @@ -167,7 +167,6 @@ pub struct OpenRouterProvider { endpoint_url: String, referer: String, title: String, - client: reqwest::blocking::Client, } impl OpenRouterProvider { @@ -178,20 +177,12 @@ impl OpenRouterProvider { let Some(api_key) = config.api_key.filter(|key| !key.trim().is_empty()) else { return Err(LlmProviderError::MissingApiKey); }; - let client = reqwest::blocking::Client::builder() - .timeout(Duration::from_secs(60)) - .build() - .map_err(|err| LlmProviderError::Http { - message: err.to_string(), - retryable: false, - })?; Ok(Self { model_id: config.model_id, api_key, endpoint_url: config.endpoint_url, referer: config.referer, title: config.title, - client, }) } @@ -211,8 +202,12 @@ impl LlmProvider for OpenRouterProvider { fn invoke(&self, request: LlmRequest) -> Result { let payload = serde_json::json!({ "model": request.model_id, - "max_completion_tokens": request.max_output_tokens, + "max_tokens": request.max_output_tokens, "temperature": 0, + "provider": { + "require_parameters": true + }, + "response_format": response_format_for_purpose(&request.purpose), "messages": [ { "role": "user", @@ -220,8 +215,14 @@ impl LlmProvider for OpenRouterProvider { } ] }); - let response = self - .client + let client = reqwest::blocking::Client::builder() + .timeout(Duration::from_secs(60)) + .build() + .map_err(|err| LlmProviderError::Http { + message: err.to_string(), + retryable: false, + })?; + let response = client .post(self.chat_completions_url()) .header("authorization", format!("Bearer {}", self.api_key)) .header("HTTP-Referer", self.referer.as_str()) @@ -273,7 +274,7 @@ impl LlmProvider for OpenRouterProvider { input_tokens: usage.prompt, output_tokens: usage.completion, total_tokens: usage.total, - cost_usd: 0.0, + cost_usd: usage.cost.unwrap_or(0.0), }) } @@ -293,6 +294,81 @@ impl LlmProvider for OpenRouterProvider { } } +fn response_format_for_purpose(purpose: &LlmPurpose) -> Value { + match purpose { + LlmPurpose::Summary => serde_json::json!({ + "type": "json_schema", + "json_schema": { + "name": "clarion_summary", + "strict": true, + "schema": { + "type": "object", + "properties": { + "purpose": { + "type": "string", + "description": "Why this entity exists in the local codebase." + }, + "behavior": { + "type": "string", + "description": "What the entity does at leaf scope." + }, + "relationships": { + "type": "string", + "description": "Important callers, callees, ownership, or adjacent entities visible from the prompt." + }, + "risks": { + "type": "string", + "description": "Notable implementation risks, caveats, or empty string when none are visible." + } + }, + "required": ["purpose", "behavior", "relationships", "risks"], + "additionalProperties": false + } + } + }), + LlmPurpose::InferredEdges => serde_json::json!({ + "type": "json_schema", + "json_schema": { + "name": "clarion_inferred_calls", + "strict": true, + "schema": { + "type": "object", + "properties": { + "edges": { + "type": "array", + "items": { + "type": "object", + "properties": { + "site_key": { + "type": "string", + "description": "The unresolved call-site key from the prompt." + }, + "target_id": { + "type": "string", + "description": "The Clarion entity id for the inferred callee." + }, + "confidence": { + "type": "number", + "description": "Model confidence from 0.0 to 1.0." + }, + "rationale": { + "type": "string", + "description": "Brief evidence for the inferred target." + } + }, + "required": ["site_key", "target_id", "confidence", "rationale"], + "additionalProperties": false + } + } + }, + "required": ["edges"], + "additionalProperties": false + } + } + }), + } +} + #[derive(Debug, Deserialize)] struct OpenRouterChatResponse { model: String, @@ -346,6 +422,7 @@ struct OpenRouterUsage { completion: u32, #[serde(rename = "total_tokens")] total: u32, + cost: Option, } #[derive(Debug, Deserialize)] @@ -442,6 +519,7 @@ pub struct InferredCallsPromptInput { pub caller_source_excerpt: String, pub unresolved_call_sites_json: String, pub candidate_entities_json: String, + pub max_edges: usize, } pub fn build_leaf_summary_prompt(input: &LeafSummaryPromptInput) -> PromptTemplate { @@ -471,11 +549,13 @@ pub fn build_inferred_calls_prompt(input: &InferredCallsPromptInput) -> PromptTe Caller source excerpt:\n{source}\n\ Unresolved call sites JSON:\n{sites}\n\ Candidate entities JSON:\n{candidates}\n\ - Return JSON with an edges array containing site_key, target_id, confidence, and rationale.", + Return JSON with an edges array containing no more than {max_edges} entries. \ + Each edge must contain site_key, target_id, confidence, and rationale.", caller = input.caller_entity_id, source = input.caller_source_excerpt, sites = input.unresolved_call_sites_json, candidates = input.candidate_entities_json, + max_edges = input.max_edges, ), } } @@ -535,10 +615,12 @@ mod tests { caller_source_excerpt: "return DISPATCH[key]()".to_owned(), unresolved_call_sites_json: r#"[{"site_key":"a"}]"#.to_owned(), candidate_entities_json: r#"[{"id":"python:function:demo.world"}]"#.to_owned(), + max_edges: 8, }); assert_eq!(inferred.id, INFERRED_CALLS_PROMPT_VERSION); assert!(inferred.body.contains("python:function:demo.via_dispatch")); assert!(inferred.body.contains("Return JSON")); + assert!(inferred.body.contains("no more than 8 entries")); } #[test] @@ -607,8 +689,15 @@ mod tests { assert!(request.contains("http-referer: https://github.com/qacona/clarion")); assert!(request.contains("x-openrouter-title: Clarion")); assert!(request.contains(r#""model":"anthropic/claude-sonnet-4.6""#)); - assert!(request.contains(r#""max_completion_tokens":512"#)); + assert!(request.contains(r#""max_tokens":512"#)); assert!(request.contains("Summarize this function")); + assert!( + request.contains(r#""response_format":{"json_schema":{"name":"clarion_summary""#) + ); + assert!(request.contains(r#""strict":true"#)); + assert!( + request.contains(r#""required":["purpose","behavior","relationships","risks"]"#) + ); let body = r#"{ "id": "gen-01", @@ -622,7 +711,7 @@ mod tests { "message": {"role": "assistant", "content": "{\"purpose\":\"demo\"}"} } ], - "usage": {"prompt_tokens": 1000, "completion_tokens": 200, "total_tokens": 1200} + "usage": {"prompt_tokens": 1000, "completion_tokens": 200, "total_tokens": 1200, "cost": 0.123} }"#; write!( stream, @@ -656,7 +745,7 @@ mod tests { assert_eq!(response.input_tokens, 1000); assert_eq!(response.output_tokens, 200); assert_eq!(response.total_tokens, 1200); - assert!((response.cost_usd - 0.0).abs() < f64::EPSILON); + assert!((response.cost_usd - 0.123).abs() < f64::EPSILON); handle.join().expect("server thread"); } @@ -709,6 +798,76 @@ mod tests { assert!(err.to_string().contains("Provider disconnected")); } + #[test] + fn openrouter_provider_uses_inferred_calls_schema_for_inferred_requests() { + use std::io::{Read, Write}; + use std::net::TcpListener; + + let listener = TcpListener::bind("127.0.0.1:0").expect("bind test server"); + let addr = listener.local_addr().expect("local addr"); + let handle = std::thread::spawn(move || { + let (mut stream, _) = listener.accept().expect("accept request"); + let mut request = [0_u8; 8192]; + let read = stream.read(&mut request).expect("read request"); + let request = String::from_utf8_lossy(&request[..read]); + assert!( + request.contains( + r#""response_format":{"json_schema":{"name":"clarion_inferred_calls""# + ) + ); + assert!(request.contains(r#""required":["edges"]"#)); + assert!( + request.contains(r#""required":["site_key","target_id","confidence","rationale"]"#) + ); + + let body = r#"{ + "id": "gen-01", + "object": "chat.completion", + "created": 1779000000, + "model": "anthropic/claude-sonnet-4.6", + "choices": [ + { + "finish_reason": "stop", + "native_finish_reason": "stop", + "message": {"role": "assistant", "content": "{\"edges\":[]}"} + } + ], + "usage": {"prompt_tokens": 10, "completion_tokens": 2, "total_tokens": 12, "cost": 0.004} + }"#; + write!( + stream, + "HTTP/1.1 200 OK\r\ncontent-type: application/json\r\ncontent-length: {}\r\n\r\n{}", + body.len(), + body + ) + .expect("write response"); + }); + let provider = OpenRouterProvider::from_config(OpenRouterProviderConfig { + api_key: Some("secret".to_owned()), + allow_live_provider: true, + model_id: "anthropic/claude-sonnet-4.6".to_owned(), + endpoint_url: format!("http://{addr}/api/v1"), + referer: "https://github.com/qacona/clarion".to_owned(), + title: "Clarion".to_owned(), + }) + .expect("test provider"); + + let response = provider + .invoke(LlmRequest { + purpose: LlmPurpose::InferredEdges, + model_id: "anthropic/claude-sonnet-4.6".to_owned(), + prompt_id: INFERRED_CALLS_PROMPT_VERSION.to_owned(), + prompt: "Resolve calls".to_owned(), + max_output_tokens: 512, + }) + .expect("invoke mocked OpenRouter"); + + assert_eq!(response.output_json, r#"{"edges":[]}"#); + assert_eq!(response.total_tokens, 12); + assert!((response.cost_usd - 0.004).abs() < f64::EPSILON); + handle.join().expect("server thread"); + } + #[test] fn openrouter_provider_connection_error_is_retryable() { let listener = std::net::TcpListener::bind("127.0.0.1:0").expect("bind unused port"); diff --git a/crates/clarion-core/src/plugin/discovery.rs b/crates/clarion-core/src/plugin/discovery.rs index a095952e..63b83b59 100644 --- a/crates/clarion-core/src/plugin/discovery.rs +++ b/crates/clarion-core/src/plugin/discovery.rs @@ -358,17 +358,17 @@ fn find_manifest(exec_path: &std::path::Path, suffix: &str) -> Result for HostError { } } -/// Informational diagnostic accumulated during a host's lifetime. -/// -/// Collected into `self.findings` on each enforcement action. Drained via -/// [`PluginHost::take_findings`]. Will eventually be persisted as ADR-004 -/// Findings; for Sprint 1 they are collected only. -#[derive(Debug, Clone)] -pub struct HostFinding { - /// Finding subcode, e.g. `"CLA-INFRA-PLUGIN-PATH-ESCAPE"`. - pub subcode: &'static str, - /// Human-readable message. - pub message: String, - /// Structured metadata (keys: `"offending_path"`, `"entity_id"`, etc.). - pub metadata: BTreeMap, -} - -impl HostFinding { - fn undeclared_kind(kind: &str, qualified_name: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("kind".to_owned(), kind.to_owned()); - metadata.insert("qualified_name".to_owned(), qualified_name.to_owned()); - Self { - subcode: FINDING_UNDECLARED_KIND, - message: format!("entity kind {kind:?} is not declared in the manifest ontology"), - metadata, - } - } - - fn entity_id_mismatch(got: &str, expected: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("got".to_owned(), got.to_owned()); - metadata.insert("expected".to_owned(), expected.to_owned()); - Self { - subcode: FINDING_ENTITY_ID_MISMATCH, - message: format!("entity id mismatch: got {got:?}, expected {expected:?}"), - metadata, - } - } - - fn path_escape(offending_path: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("offending_path".to_owned(), offending_path.to_owned()); - Self { - subcode: FINDING_PATH_ESCAPE, - message: format!("entity source path escapes project root: {offending_path:?}"), - metadata, - } - } - - fn disabled_path_escape() -> Self { - Self { - subcode: FINDING_DISABLED_PATH_ESCAPE, - message: "path-escape circuit breaker tripped; plugin killed".to_owned(), - metadata: BTreeMap::new(), - } - } - - fn entity_cap_exceeded_finding(cap: usize, would_reach: usize) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("cap".to_owned(), cap.to_string()); - metadata.insert("would_reach".to_owned(), would_reach.to_string()); - Self { - subcode: FINDING_ENTITY_CAP, - message: format!("entity cap {cap} would be exceeded (would reach {would_reach})"), - metadata, - } - } - - fn unsupported_capability(msg: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("detail".to_owned(), msg.to_owned()); - Self { - subcode: FINDING_UNSUPPORTED_CAPABILITY, - message: format!("manifest has unsupported capability: {msg}"), - metadata, - } - } - - fn non_utf8_path(lossy_repr: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("path_lossy".to_owned(), lossy_repr.to_owned()); - Self { - subcode: FINDING_NON_UTF8_PATH, - message: format!( - "file skipped: path is not valid UTF-8 and cannot be expressed \ - on the JSON wire protocol: {lossy_repr:?}" - ), - metadata, - } - } - - fn malformed_entity(serde_err: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("serde_error".to_owned(), serde_err.to_owned()); - Self { - subcode: FINDING_MALFORMED_ENTITY, - message: format!("plugin emitted an entity that failed to deserialise: {serde_err}"), - metadata, - } - } - - fn malformed_edge(serde_err: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("serde_error".to_owned(), serde_err.to_owned()); - Self { - subcode: FINDING_MALFORMED_EDGE, - message: format!("plugin emitted an edge that failed to deserialise: {serde_err}"), - metadata, - } - } - - fn undeclared_edge_kind(kind: &str, from_id: &str, to_id: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("kind".to_owned(), kind.to_owned()); - metadata.insert("from_id".to_owned(), from_id.to_owned()); - metadata.insert("to_id".to_owned(), to_id.to_owned()); - Self { - subcode: FINDING_UNDECLARED_EDGE_KIND, - message: format!("edge kind {kind:?} is not declared in the manifest ontology"), - metadata, - } - } - - fn edge_field_oversize(field: &'static str, actual_bytes: usize) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("field".to_owned(), field.to_owned()); - metadata.insert("actual_bytes".to_owned(), actual_bytes.to_string()); - metadata.insert("limit_bytes".to_owned(), MAX_ENTITY_FIELD_BYTES.to_string()); - Self { - subcode: FINDING_EDGE_FIELD_OVERSIZE, - message: format!( - "edge field {field:?} is {actual_bytes} bytes, over the {MAX_ENTITY_FIELD_BYTES}-byte limit" - ), - metadata, - } - } - - fn malformed_unresolved_call_site(site: &UnresolvedCallSite, reason: &str) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("caller_entity_id".to_owned(), site.caller_entity_id.clone()); - metadata.insert("site_ordinal".to_owned(), site.site_ordinal.to_string()); - metadata.insert( - "source_byte_start".to_owned(), - site.source_byte_start.to_string(), - ); - metadata.insert( - "source_byte_end".to_owned(), - site.source_byte_end.to_string(), - ); - metadata.insert("reason".to_owned(), reason.to_owned()); - Self { - subcode: FINDING_MALFORMED_UNRESOLVED_CALL_SITE, - message: format!("plugin emitted malformed unresolved call site: {reason}"), - metadata, - } - } - - fn entity_field_oversize(field: &'static str, actual_bytes: usize) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("field".to_owned(), field.to_owned()); - metadata.insert("actual_bytes".to_owned(), actual_bytes.to_string()); - metadata.insert("limit_bytes".to_owned(), MAX_ENTITY_FIELD_BYTES.to_string()); - Self { - subcode: FINDING_ENTITY_FIELD_OVERSIZE, - message: format!( - "entity field {field:?} is {actual_bytes} bytes, over the {MAX_ENTITY_FIELD_BYTES}-byte limit" - ), - metadata, - } - } - - /// Emitted by the CLI wrapper once the child has been reaped and its exit - /// status indicates a signal consistent with an `RLIMIT_AS` kill (SIGKILL - /// or SIGSEGV). Lives on [`HostFinding`] rather than being constructed in - /// the CLI so the finding-subcode API is centralised. - pub fn oom_killed(plugin_id: &str, signal: i32) -> Self { - let mut metadata = BTreeMap::new(); - metadata.insert("plugin_id".to_owned(), plugin_id.to_owned()); - metadata.insert("signal".to_owned(), signal.to_string()); - Self { - subcode: FINDING_OOM_KILLED, - message: format!( - "plugin {plugin_id} killed by signal {signal} \ - (likely RLIMIT_AS enforcement per ADR-021 §2d)" - ), - metadata, - } - } -} - // ── PluginHost ──────────────────────────────────────────────────────────────── /// Supervisor managing a single plugin connection. @@ -1101,8 +845,9 @@ impl PluginHost { // `properties_json` downstream. Oversize in any field drops // the entity without killing the plugin. if let Some((field, len)) = oversize_field(&raw) { - self.findings - .push(HostFinding::entity_field_oversize(field, len)); + let finding = + HostFinding::entity_field_oversize(field, len, MAX_ENTITY_FIELD_BYTES); + self.findings.push(finding); continue; } @@ -1229,8 +974,8 @@ impl PluginHost { } }; if let Some((field, len)) = oversize_edge_field(&raw) { - self.findings - .push(HostFinding::edge_field_oversize(field, len)); + let finding = HostFinding::edge_field_oversize(field, len, MAX_ENTITY_FIELD_BYTES); + self.findings.push(finding); continue; } if !declared_edge_kinds.contains(&raw.kind) { @@ -1455,6 +1200,9 @@ mod tests { use tempfile::TempDir; use super::*; + use crate::plugin::limits::{ + FINDING_DISABLED_PATH_ESCAPE, FINDING_ENTITY_CAP, FINDING_PATH_ESCAPE, + }; use crate::plugin::mock::MockPlugin; use crate::plugin::{AnalyzeFileParams, InitializeParams}; diff --git a/crates/clarion-core/src/plugin/host_findings.rs b/crates/clarion-core/src/plugin/host_findings.rs new file mode 100644 index 00000000..d93206c0 --- /dev/null +++ b/crates/clarion-core/src/plugin/host_findings.rs @@ -0,0 +1,273 @@ +//! Host-level finding subcodes and constructors. +//! +//! Resource and framing findings live in `limits.rs` next to the types they +//! reference (`ContentLengthCeiling`, `EntityCountCap`, etc.). The subcodes +//! here cover protocol, ontology, and manifest-capability failures that belong +//! to the supervisor layer. + +use std::collections::BTreeMap; + +use crate::plugin::limits::{ + FINDING_DISABLED_PATH_ESCAPE, FINDING_ENTITY_CAP, FINDING_OOM_KILLED, FINDING_PATH_ESCAPE, +}; +use crate::plugin::protocol::UnresolvedCallSite; + +/// Emitted when a plugin emits an entity whose `kind` is not in the manifest's +/// `entity_kinds` list (ADR-022 ontology boundary). +pub const FINDING_UNDECLARED_KIND: &str = "CLA-INFRA-PLUGIN-UNDECLARED-KIND"; + +/// Emitted when a plugin emits an entity whose `id` string does not match the +/// expected `entity_id(plugin_id, kind, qualified_name)` (UQ-WP2-11). +pub const FINDING_ENTITY_ID_MISMATCH: &str = "CLA-INFRA-PLUGIN-ENTITY-ID-MISMATCH"; + +/// Emitted when the manifest contains a capability not supported in v0.1 +/// (ADR-021 §Layer 1). +pub const FINDING_UNSUPPORTED_CAPABILITY: &str = "CLA-INFRA-MANIFEST-UNSUPPORTED-CAPABILITY"; + +/// Emitted when a plugin returns an entity whose JSON shape fails to +/// deserialise into `RawEntity` (missing required field, wrong type, etc.). +/// +/// Structurally invalid entities are dropped rather than failing the run, so +/// the finding is the only signal the operator gets that the plugin emitted +/// malformed output. Without this, a plugin bug that silently produces garbage +/// for a subset of entities looks identical to "no entities found". +pub const FINDING_MALFORMED_ENTITY: &str = "CLA-INFRA-PLUGIN-MALFORMED-ENTITY"; + +/// Emitted when the host is asked to analyze a file whose path is not +/// representable as UTF-8. The wire protocol is JSON (UTF-8 only), so the host +/// cannot forward the path to the plugin; the file is skipped with this finding +/// and the run continues. +/// +/// Linux filenames are arbitrary byte sequences. Using `to_string_lossy` at +/// the wire boundary would replace invalid bytes with U+FFFD, yielding a path +/// the plugin cannot open and an obscure "plugin returned no entities" symptom. +/// Failing loudly with this finding keeps the diagnostic at the host layer. +pub const FINDING_NON_UTF8_PATH: &str = "CLA-INFRA-HOST-NON-UTF8-PATH"; + +/// Emitted when a plugin returns an entity with a string field longer than +/// `MAX_ENTITY_FIELD_BYTES`. Entity is dropped; plugin is not killed. +/// +/// Without this bound, a plugin could emit up to `EntityCountCap` entities each +/// carrying multi-MB `qualified_name`/`kind`/`id`/`file_path` strings. The +/// identity check duplicates `qualified_name` through `format!()`, so the memory +/// cost is at least 2x the incoming string per offending entity, making this a +/// RAM-amplification vector even under the 8 MiB Content-Length ceiling. +pub const FINDING_ENTITY_FIELD_OVERSIZE: &str = "CLA-INFRA-PLUGIN-ENTITY-FIELD-OVERSIZE"; + +/// Emitted when a plugin returns an edge whose JSON shape fails to deserialise +/// into `RawEdge` (missing required field, wrong type, etc.). Symmetric with +/// [`FINDING_MALFORMED_ENTITY`]; edge is dropped, run continues. +pub const FINDING_MALFORMED_EDGE: &str = "CLA-INFRA-PLUGIN-MALFORMED-EDGE"; + +/// Emitted when a plugin emits an edge whose `kind` is not in the manifest's +/// `edge_kinds` list (ADR-022 ontology boundary, edge variant). Drop + finding; +/// no kill. +pub const FINDING_UNDECLARED_EDGE_KIND: &str = "CLA-INFRA-PLUGIN-UNDECLARED-EDGE-KIND"; + +/// Emitted when a plugin returns an edge with a string field longer than +/// `MAX_ENTITY_FIELD_BYTES`. Edge is dropped; plugin is not killed. Same +/// rationale as [`FINDING_ENTITY_FIELD_OVERSIZE`] (RAM amplification). +pub const FINDING_EDGE_FIELD_OVERSIZE: &str = "CLA-INFRA-PLUGIN-EDGE-FIELD-OVERSIZE"; + +/// Emitted when `stats.unresolved_call_sites` contains a row that cannot be +/// tied back to the accepted entities and source bytes for this `analyze_file` +/// response. The row is dropped; aggregate counters are retained. +pub const FINDING_MALFORMED_UNRESOLVED_CALL_SITE: &str = + "CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE"; + +/// Informational diagnostic accumulated during a host's lifetime. +/// +/// Collected into `self.findings` on each enforcement action. Drained via +/// `PluginHost::take_findings`. Will eventually be persisted as ADR-004 +/// Findings; for Sprint 1 they are collected only. +#[derive(Debug, Clone)] +pub struct HostFinding { + /// Finding subcode, e.g. `"CLA-INFRA-PLUGIN-PATH-ESCAPE"`. + pub subcode: &'static str, + /// Human-readable message. + pub message: String, + /// Structured metadata (keys: `"offending_path"`, `"entity_id"`, etc.). + pub metadata: BTreeMap, +} + +impl HostFinding { + pub(super) fn undeclared_kind(kind: &str, qualified_name: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("kind".to_owned(), kind.to_owned()); + metadata.insert("qualified_name".to_owned(), qualified_name.to_owned()); + Self { + subcode: FINDING_UNDECLARED_KIND, + message: format!("entity kind {kind:?} is not declared in the manifest ontology"), + metadata, + } + } + + pub(super) fn entity_id_mismatch(got: &str, expected: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("got".to_owned(), got.to_owned()); + metadata.insert("expected".to_owned(), expected.to_owned()); + Self { + subcode: FINDING_ENTITY_ID_MISMATCH, + message: format!("entity id mismatch: got {got:?}, expected {expected:?}"), + metadata, + } + } + + pub(super) fn path_escape(offending_path: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("offending_path".to_owned(), offending_path.to_owned()); + Self { + subcode: FINDING_PATH_ESCAPE, + message: format!("entity source path escapes project root: {offending_path:?}"), + metadata, + } + } + + pub(super) fn disabled_path_escape() -> Self { + Self { + subcode: FINDING_DISABLED_PATH_ESCAPE, + message: "path-escape circuit breaker tripped; plugin killed".to_owned(), + metadata: BTreeMap::new(), + } + } + + pub(super) fn entity_cap_exceeded_finding(cap: usize, would_reach: usize) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("cap".to_owned(), cap.to_string()); + metadata.insert("would_reach".to_owned(), would_reach.to_string()); + Self { + subcode: FINDING_ENTITY_CAP, + message: format!("entity cap {cap} would be exceeded (would reach {would_reach})"), + metadata, + } + } + + pub(super) fn unsupported_capability(msg: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("detail".to_owned(), msg.to_owned()); + Self { + subcode: FINDING_UNSUPPORTED_CAPABILITY, + message: format!("manifest has unsupported capability: {msg}"), + metadata, + } + } + + pub(super) fn non_utf8_path(lossy_repr: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("path_lossy".to_owned(), lossy_repr.to_owned()); + Self { + subcode: FINDING_NON_UTF8_PATH, + message: format!( + "file skipped: path is not valid UTF-8 and cannot be expressed \ + on the JSON wire protocol: {lossy_repr:?}" + ), + metadata, + } + } + + pub(super) fn malformed_entity(serde_err: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("serde_error".to_owned(), serde_err.to_owned()); + Self { + subcode: FINDING_MALFORMED_ENTITY, + message: format!("plugin emitted an entity that failed to deserialise: {serde_err}"), + metadata, + } + } + + pub(super) fn malformed_edge(serde_err: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("serde_error".to_owned(), serde_err.to_owned()); + Self { + subcode: FINDING_MALFORMED_EDGE, + message: format!("plugin emitted an edge that failed to deserialise: {serde_err}"), + metadata, + } + } + + pub(super) fn undeclared_edge_kind(kind: &str, from_id: &str, to_id: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("kind".to_owned(), kind.to_owned()); + metadata.insert("from_id".to_owned(), from_id.to_owned()); + metadata.insert("to_id".to_owned(), to_id.to_owned()); + Self { + subcode: FINDING_UNDECLARED_EDGE_KIND, + message: format!("edge kind {kind:?} is not declared in the manifest ontology"), + metadata, + } + } + + pub(super) fn edge_field_oversize( + field: &'static str, + actual_bytes: usize, + limit_bytes: usize, + ) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("field".to_owned(), field.to_owned()); + metadata.insert("actual_bytes".to_owned(), actual_bytes.to_string()); + metadata.insert("limit_bytes".to_owned(), limit_bytes.to_string()); + Self { + subcode: FINDING_EDGE_FIELD_OVERSIZE, + message: format!( + "edge field {field:?} is {actual_bytes} bytes, over the {limit_bytes}-byte limit" + ), + metadata, + } + } + + pub(super) fn malformed_unresolved_call_site(site: &UnresolvedCallSite, reason: &str) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("caller_entity_id".to_owned(), site.caller_entity_id.clone()); + metadata.insert("site_ordinal".to_owned(), site.site_ordinal.to_string()); + metadata.insert( + "source_byte_start".to_owned(), + site.source_byte_start.to_string(), + ); + metadata.insert( + "source_byte_end".to_owned(), + site.source_byte_end.to_string(), + ); + metadata.insert("reason".to_owned(), reason.to_owned()); + Self { + subcode: FINDING_MALFORMED_UNRESOLVED_CALL_SITE, + message: format!("plugin emitted malformed unresolved call site: {reason}"), + metadata, + } + } + + pub(super) fn entity_field_oversize( + field: &'static str, + actual_bytes: usize, + limit_bytes: usize, + ) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("field".to_owned(), field.to_owned()); + metadata.insert("actual_bytes".to_owned(), actual_bytes.to_string()); + metadata.insert("limit_bytes".to_owned(), limit_bytes.to_string()); + Self { + subcode: FINDING_ENTITY_FIELD_OVERSIZE, + message: format!( + "entity field {field:?} is {actual_bytes} bytes, over the {limit_bytes}-byte limit" + ), + metadata, + } + } + + /// Emitted by the CLI wrapper once the child has been reaped and its exit + /// status indicates a signal consistent with an `RLIMIT_AS` kill (SIGKILL + /// or SIGSEGV). Lives on [`HostFinding`] rather than being constructed in + /// the CLI so the finding-subcode API is centralised. + pub fn oom_killed(plugin_id: &str, signal: i32) -> Self { + let mut metadata = BTreeMap::new(); + metadata.insert("plugin_id".to_owned(), plugin_id.to_owned()); + metadata.insert("signal".to_owned(), signal.to_string()); + Self { + subcode: FINDING_OOM_KILLED, + message: format!( + "plugin {plugin_id} killed by signal {signal} \ + (likely RLIMIT_AS enforcement per ADR-021 §2d)" + ), + metadata, + } + } +} diff --git a/crates/clarion-core/src/plugin/jail.rs b/crates/clarion-core/src/plugin/jail.rs index eef2a8a5..bfb855e1 100644 --- a/crates/clarion-core/src/plugin/jail.rs +++ b/crates/clarion-core/src/plugin/jail.rs @@ -63,6 +63,13 @@ pub enum JailError { /// - `Ok(canonical_candidate)` — the resolved, confirmed-safe path. /// - `Err(JailError::EscapedRoot)` — `candidate` resolves outside `root`. /// - `Err(JailError::Io)` — either path does not exist or cannot be resolved. +/// +/// The returned path is a membership proof at canonicalization time, not a +/// durable file handle. Code that later opens or serves the path must account +/// for filesystem races between this check and the later open. Use an +/// `openat`-style strategy anchored to a pinned root descriptor, or re-run the +/// jail check after opening and compare against the canonical path accepted +/// here. pub fn jail(root: &Path, candidate: &Path) -> Result { let canonical_root = std::fs::canonicalize(root)?; let canonical_candidate = std::fs::canonicalize(candidate)?; @@ -133,7 +140,7 @@ mod tests { /// A path constructed with `..` that resolves *above* the root must be /// rejected. `std::fs::canonicalize` resolves the `..` before the - /// `starts_with` check, so there is no TOCTOU window. + /// `starts_with` check, so lexical parent segments cannot bypass the jail. #[test] fn jail_02_dotdot_escape_returns_escaped_root() { let root = TempDir::new().expect("tmpdir"); diff --git a/crates/clarion-core/src/plugin/limits.rs b/crates/clarion-core/src/plugin/limits.rs index 9f0dc40d..debe30e1 100644 --- a/crates/clarion-core/src/plugin/limits.rs +++ b/crates/clarion-core/src/plugin/limits.rs @@ -530,14 +530,34 @@ mod tests { /// On Linux: calling `apply_prlimit_as` with the default ceiling returns Ok. /// - /// This sets `RLIMIT_AS` on the test process itself, which is safe — tests - /// run well under 2 GiB. Note: this test sets **both the soft and hard** - /// `RLIMIT_AS` to `DEFAULT_MAX_RSS_MIB` (2 GiB) on the test binary's - /// process. Any subsequent test in the same binary cannot raise the limit - /// above 2 GiB without root privileges. + /// `setrlimit` lowers the current process hard limit, so the actual syscall + /// probe runs in a child test process. That keeps default parallel test runs + /// from starving sibling tests after this probe succeeds. #[cfg(target_os = "linux")] #[test] fn apply_prlimit_linux_returns_ok() { + let output = std::process::Command::new(std::env::current_exe().expect("current exe")) + .args([ + "--exact", + "plugin::limits::tests::apply_prlimit_linux_child_process_returns_ok", + "--ignored", + "--nocapture", + ]) + .output() + .expect("spawn child prlimit test"); + assert!( + output.status.success(), + "child prlimit test failed with status {}\nstdout:\n{}\nstderr:\n{}", + output.status, + String::from_utf8_lossy(&output.stdout), + String::from_utf8_lossy(&output.stderr) + ); + } + + #[cfg(target_os = "linux")] + #[test] + #[ignore = "invoked by apply_prlimit_linux_returns_ok in a child process"] + fn apply_prlimit_linux_child_process_returns_ok() { let result = apply_prlimit_as(DEFAULT_MAX_RSS_MIB); assert!(result.is_ok(), "apply_prlimit_as must succeed: {result:?}"); } diff --git a/crates/clarion-core/src/plugin/manifest.rs b/crates/clarion-core/src/plugin/manifest.rs index 35fbcbd2..65518351 100644 --- a/crates/clarion-core/src/plugin/manifest.rs +++ b/crates/clarion-core/src/plugin/manifest.rs @@ -25,7 +25,7 @@ use crate::entity_id::validate_kind_grammar; // ── Reserved lists (ADR-022) ────────────────────────────────────────────────── /// Entity kinds the core owns; plugins may not declare these (ADR-022 §Core owns). -const RESERVED_ENTITY_KINDS: &[&str] = &["file", "subsystem", "guidance"]; +pub const RESERVED_ENTITY_KINDS: &[&str] = &["file", "subsystem", "guidance"]; /// Rule-ID prefixes the core owns; plugins may not claim these (ADR-022 §Core owns). /// @@ -41,6 +41,7 @@ const RESERVED_RULE_ID_PREFIXES: &[&str] = &["CLA-INFRA-", "CLA-FACT-"]; /// surfaces in the `initialize` handshake reply. Use [`ManifestError::subcode`] to /// obtain the machine-readable finding code. #[derive(Debug, Error, PartialEq, Eq)] +#[non_exhaustive] pub enum ManifestError { /// TOML parse failure or a required field is absent. /// @@ -49,7 +50,7 @@ pub enum ManifestError { Malformed { message: String }, /// An identifier string fails the ADR-022 grammar `[a-z][a-z0-9_]*` (kinds) - /// or `CLA-[A-Z]+(-[A-Z0-9]+)*-` (rule-ID prefix). + /// or `CLA-[A-Z]+(-[A-Z0-9]+)+-` (rule-ID prefix). /// /// Finding code: `CLA-INFRA-MANIFEST-MALFORMED`. #[error("CLA-INFRA-MANIFEST-MALFORMED: {field} {value:?} violates ADR-022 identifier grammar")] @@ -122,8 +123,9 @@ pub struct Manifest { /// `[ontology]` table. pub ontology: Ontology, - /// `[integrations.*]` — optional, opaque passthrough for plugin-specific - /// integration config (e.g. WP3's `[integrations.wardline]`). + /// `[integrations.*]` — optional string-valued passthrough for + /// plugin-specific integration config (e.g. WP3's + /// `[integrations.wardline]`). /// /// The core does not interpret this table; it is preserved so Task 6 can /// forward it to the plugin during `initialize` if needed. @@ -131,7 +133,7 @@ pub struct Manifest { /// Entry count is capped at [`MAX_INTEGRATIONS`] at parse time — see /// [`parse_manifest`]. #[serde(default)] - pub integrations: BTreeMap, + pub integrations: BTreeMap>, } /// Maximum number of `[integrations.*]` entries accepted per manifest. @@ -232,7 +234,7 @@ pub struct Ontology { pub edge_kinds: Vec, /// Rule-ID prefix, e.g. `"CLA-PY-"`. Must end with `-` and match - /// `CLA-[A-Z]+(-[A-Z0-9]+)*-`. Must not be a core-reserved prefix. + /// `CLA-[A-Z]+(-[A-Z0-9]+)+-`. Must not be a core-reserved prefix. pub rule_id_prefix: String, /// Ontology version (semver). Bumped when entity/edge/rule set changes. @@ -401,10 +403,12 @@ fn validate_kind_string(field: &'static str, value: &str) -> Result<(), Manifest /// /// Rules: /// 1. Must end with `-`. -/// 2. Strip the trailing `-`; the remainder must match `CLA-[A-Z]+(-[A-Z0-9]+)*`. +/// 2. Strip the trailing `-`; the remainder must match `CLA-[A-Z]+(-[A-Z0-9]+)+` +/// (one-or-more `-[A-Z0-9]+` segments after `CLA`, per ADR-022). /// Implementation: split on `-`, verify the first segment is `CLA`, and each /// subsequent non-empty segment is `[A-Z0-9]+` (ASCII uppercase or digit). -/// There must be at least one segment after `CLA` (so `CLA-` alone is invalid). +/// The `segments.len() < 2` guard below is how the `+` quantifier is enforced +/// without a regex engine — `CLA-` alone has only one segment and is rejected. /// /// Examples of valid prefixes: `CLA-PY-`, `CLA-JAVA-`, `CLA-FOO-BAR-`. /// Examples of invalid prefixes: `PY-`, `cla-py-`, `CLA-py-`, `CLA-PY` (no trailing @@ -490,6 +494,46 @@ rule_id_prefix = "CLA-PY-" ontology_version = "0.1.0" "#; + fn manifest_with(field_override: &str) -> String { + let (field, _) = field_override + .split_once('=') + .expect("override is a TOML key/value line"); + let field = field.trim(); + let prefix = format!("{field} ="); + let mut replaced = false; + let lines = VALID_MANIFEST + .lines() + .map(|line| { + if line.trim_start().starts_with(&prefix) { + replaced = true; + field_override.to_owned() + } else { + line.to_owned() + } + }) + .collect::>(); + assert!(replaced, "field {field:?} exists in VALID_MANIFEST"); + lines.join("\n") + } + + fn manifest_without(field: &str) -> String { + let prefix = format!("{field} ="); + let mut removed = false; + let lines = VALID_MANIFEST + .lines() + .filter_map(|line| { + if line.trim_start().starts_with(&prefix) { + removed = true; + None + } else { + Some(line.to_owned()) + } + }) + .collect::>(); + assert!(removed, "field {field:?} exists in VALID_MANIFEST"); + lines.join("\n") + } + // ── Positive: full parse ────────────────────────────────────────────────── #[test] @@ -607,14 +651,21 @@ max_version = "1.0.0" "#; let manifest = parse_manifest(toml.as_bytes()).unwrap(); // The integrations table is present; the core does not interpret it. - assert!(manifest.integrations.contains_key("wardline")); + let wardline: &BTreeMap = manifest + .integrations + .get("wardline") + .expect("wardline integration"); + assert_eq!( + wardline.get("min_version").map(String::as_str), + Some("0.1.0") + ); } // ── Negative: too many [integrations.*] entries ─────────────────────────── /// A `plugin.toml` with more than [`MAX_INTEGRATIONS`] entries is rejected /// as `Malformed` — prevents an attacker-controlled manifest from forcing - /// the host to retain an unbounded `BTreeMap` for + /// the host to retain an unbounded integrations map for /// the run lifetime. #[test] fn negative_integrations_above_cap_is_rejected() { @@ -696,27 +747,7 @@ ontology_version = "0.1.0" fn negative_missing_plugin_id_returns_malformed() { // A manifest without [plugin].plugin_id must fail deserialization because // plugin_id is a required field (no serde default). - let toml = r#" -[plugin] -name = "my-plugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_without("plugin_id"); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!(err, ManifestError::Malformed { .. })); @@ -729,28 +760,7 @@ ontology_version = "0.1.0" // "my-plugin" contains a hyphen; the ADR-022 kind grammar [a-z][a-z0-9_]* // forbids it. This is the exact contradiction that motivated separating // plugin_id from name. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "my-plugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"plugin_id = "my-plugin""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -766,26 +776,7 @@ ontology_version = "0.1.0" #[test] fn negative_missing_plugin_name_returns_malformed() { - let toml = r#" -[plugin] -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_without("name"); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!(err, ManifestError::Malformed { .. })); @@ -795,28 +786,7 @@ ontology_version = "0.1.0" #[test] fn negative_zero_rss_mb_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 0 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with("expected_max_rss_mb = 0"); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!( @@ -828,28 +798,7 @@ ontology_version = "0.1.0" #[test] fn negative_empty_entity_kinds_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = [] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with("entity_kinds = []"); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!( @@ -861,28 +810,7 @@ ontology_version = "0.1.0" #[test] fn negative_entity_kind_uppercase_is_grammar_violation() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["Function"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"entity_kinds = ["Function"]"#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -893,28 +821,7 @@ ontology_version = "0.1.0" #[test] fn negative_entity_kind_hyphen_is_grammar_violation() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["func-tion"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"entity_kinds = ["func-tion"]"#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -925,28 +832,7 @@ ontology_version = "0.1.0" #[test] fn negative_entity_kind_digit_prefix_is_grammar_violation() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["1function"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"entity_kinds = ["1function"]"#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -960,28 +846,7 @@ ontology_version = "0.1.0" #[test] fn negative_rule_id_prefix_no_cla_prefix_rejected() { // "PY-" — does not start with CLA. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "PY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "PY-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -993,28 +858,7 @@ ontology_version = "0.1.0" #[test] fn negative_rule_id_prefix_lowercase_rejected() { // "cla-py-" — lowercase is invalid. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "cla-py-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "cla-py-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -1026,28 +870,7 @@ ontology_version = "0.1.0" #[test] fn negative_rule_id_prefix_mixed_case_segment_rejected() { // "CLA-py-" — mixed-case segment after CLA. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-py-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA-py-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -1060,28 +883,7 @@ ontology_version = "0.1.0" #[test] fn negative_reserved_entity_kind_file_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["file", "widget"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"entity_kinds = ["file", "widget"]"#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-RESERVED-KIND"); assert!(matches!( @@ -1092,28 +894,7 @@ ontology_version = "0.1.0" #[test] fn negative_reserved_entity_kind_subsystem_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["subsystem"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"entity_kinds = ["subsystem"]"#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-RESERVED-KIND"); assert!(matches!( @@ -1124,28 +905,7 @@ ontology_version = "0.1.0" #[test] fn negative_reserved_entity_kind_guidance_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["guidance"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"entity_kinds = ["guidance"]"#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-RESERVED-KIND"); assert!(matches!( @@ -1158,28 +918,7 @@ ontology_version = "0.1.0" #[test] fn negative_reserved_prefix_cla_infra_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-INFRA-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA-INFRA-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-RULE-ID-NAMESPACE"); assert!(matches!( @@ -1190,28 +929,7 @@ ontology_version = "0.1.0" #[test] fn negative_reserved_prefix_cla_fact_rejected() { - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-FACT-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA-FACT-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-RULE-ID-NAMESPACE"); assert!(matches!( @@ -1225,28 +943,7 @@ ontology_version = "0.1.0" #[test] fn negative_reads_outside_project_root_flagged_by_validator() { // The parser accepts this field faithfully; the validator rejects it. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = true - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-MY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with("reads_outside_project_root = true"); // parse_manifest must succeed — the parser does not reject this field. let manifest = parse_manifest(toml.as_bytes()).unwrap(); assert!(manifest.capabilities.runtime.reads_outside_project_root); @@ -1306,28 +1003,7 @@ ontology_version = "0.1.0" #[test] fn negative_rule_id_prefix_no_trailing_hyphen_rejected() { // "CLA-PY" — missing trailing `-`. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-PY" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA-PY""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -1342,28 +1018,7 @@ ontology_version = "0.1.0" #[test] fn negative_rule_id_prefix_empty_inner_segment_rejected() { // "CLA--PY-" — empty segment between hyphens. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA--PY-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA--PY-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -1378,28 +1033,7 @@ ontology_version = "0.1.0" #[test] fn negative_rule_id_prefix_only_cla_rejected() { // "CLA-" — no segment after CLA. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA-""#); let err = parse_manifest(toml.as_bytes()).unwrap_err(); assert_eq!(err.subcode(), "CLA-INFRA-MANIFEST-MALFORMED"); assert!(matches!( @@ -1414,28 +1048,7 @@ ontology_version = "0.1.0" #[test] fn positive_multi_segment_rule_id_prefix_valid() { // "CLA-FOO-BAR-" — valid multi-segment prefix. - let toml = r#" -[plugin] -name = "my-plugin" -plugin_id = "myplugin" -version = "0.1.0" -protocol_version = "1.0" -executable = "my-plugin" -language = "mylang" -extensions = ["my"] - -[capabilities.runtime] -expected_max_rss_mb = 256 -expected_entities_per_file = 100 -wardline_aware = false -reads_outside_project_root = false - -[ontology] -entity_kinds = ["widget"] -edge_kinds = [] -rule_id_prefix = "CLA-FOO-BAR-" -ontology_version = "0.1.0" -"#; + let toml = manifest_with(r#"rule_id_prefix = "CLA-FOO-BAR-""#); let manifest = parse_manifest(toml.as_bytes()).unwrap(); assert_eq!(manifest.ontology.rule_id_prefix, "CLA-FOO-BAR-"); } diff --git a/crates/clarion-core/src/plugin/mock.rs b/crates/clarion-core/src/plugin/mock.rs index a2764dac..f9e0a5d8 100644 --- a/crates/clarion-core/src/plugin/mock.rs +++ b/crates/clarion-core/src/plugin/mock.rs @@ -73,12 +73,15 @@ pub enum MockError { /// Transitions: /// ```text /// Fresh ──(initialize response sent)──► Initialized +/// └─(oversize corrupt frame sent)─► Fresh [terminal Oversize branch] /// Initialized ──(initialized notification received)──► Ready [Compliant] /// ──► Crashed [Crashing] /// Ready ──(shutdown response sent)──► ShutdownRequested /// ShutdownRequested ──(exit notification received)──► Exited /// * ──(exit notification received)──► Exited [shortcut] /// Crashed ── all further frames silently dropped +/// Oversize remains Fresh; repeated initialize requests append another corrupt +/// Content-Length frame and never advance to Initialized. /// ``` #[derive(Debug, Clone, PartialEq, Eq)] enum MockState { @@ -543,10 +546,9 @@ impl MockPlugin { fn write_response(&mut self, env: &ResponseEnvelope) -> Result<(), MockError> { let body = serde_json::to_vec(env)?; let frame = Frame { body }; - // Append to the outbox vec without disturbing the read position. - let mut tmp: Vec = Vec::new(); - write_frame(&mut tmp, &frame)?; - self.outbox.get_mut().extend_from_slice(&tmp); + // Append to the underlying buffer without disturbing the cursor's read + // position; `get_mut()` gives us the Vec directly, not the Cursor. + write_frame(self.outbox.get_mut(), &frame)?; Ok(()) } } @@ -576,6 +578,29 @@ mod tests { write_frame(mock.stdin(), &Frame { body }).expect("write_frame"); } + fn initialize_and_notify(mock: &mut MockPlugin) -> ResponseEnvelope { + send_request( + mock, + "initialize", + &InitializeParams { + protocol_version: "1.0".into(), + project_root: "/tmp/x".to_owned(), + }, + 1, + ); + mock.tick().expect("tick after initialize"); + + let frame = read_frame(mock.stdout(), ContentLengthCeiling::new(1024 * 1024)) + .expect("read initialize response"); + let response: ResponseEnvelope = + serde_json::from_slice(&frame.body).expect("deserialise initialize ResponseEnvelope"); + assert!(matches!(response.payload, ResponsePayload::Result(_))); + + send_notification(mock, "initialized", &InitializedNotification {}); + mock.tick().expect("tick after initialized notification"); + response + } + // ── Mandatory test: compliant mock completes handshake ──────────────────── /// Spec-mandated test (Task 3, §required test). @@ -633,25 +658,7 @@ mod tests { fn compliant_mock_returns_one_entity_on_analyze_file() { let mut mock = MockPlugin::new_compliant(); - // Full handshake first. - send_request( - &mut mock, - "initialize", - &InitializeParams { - protocol_version: "1.0".into(), - project_root: "/tmp/x".to_owned(), - }, - 1, - ); - mock.tick().expect("tick after initialize"); - - // Drain the initialize response frame so the cursor is ready for more. - read_frame(mock.stdout(), ContentLengthCeiling::new(1024 * 1024)) - .expect("read initialize response"); - - // Send initialized notification; mock transitions to Ready. - send_notification(&mut mock, "initialized", &InitializedNotification {}); - mock.tick().expect("tick after initialized notification"); + initialize_and_notify(&mut mock); // Send analyze_file request. send_request( @@ -691,32 +698,9 @@ mod tests { fn crashing_mock_produces_no_response_after_initialized() { let mut mock = MockPlugin::new_crashing(); - // Handshake: initialize request. - send_request( - &mut mock, - "initialize", - &InitializeParams { - protocol_version: "1.0".into(), - project_root: "/tmp/x".to_owned(), - }, - 1, - ); - mock.tick().expect("tick after initialize"); - - // Drain the initialize response. - let frame = read_frame(mock.stdout(), ContentLengthCeiling::new(1024 * 1024)) - .expect("read initialize response"); - let resp: ResponseEnvelope = serde_json::from_slice(&frame.body).unwrap(); - assert!(matches!(resp.payload, ResponsePayload::Result(_))); - - // Record the outbox position after the initialize response; no new bytes - // should appear after the crash. + initialize_and_notify(&mut mock); let pos_after_init = mock.stdout().position(); - // Send initialized notification — this triggers the crash transition. - send_notification(&mut mock, "initialized", &InitializedNotification {}); - mock.tick().expect("tick after initialized notification"); - // Send analyze_file — should be silently dropped. send_request( &mut mock, @@ -730,18 +714,13 @@ mod tests { .expect("tick after analyze_file (crashing mock)"); // The outbox must not have grown past the initialize response. - let pos_after_crash = mock.stdout().position(); - let outbox_len = mock.stdout().get_ref().len() as u64; + let outbox_len = u64::try_from(mock.stdout().get_ref().len()) + .expect("outbox length exceeds u64::MAX — impossible on any current target"); assert_eq!( outbox_len, pos_after_init, "crashing mock must not write any bytes after the initialize response; \ outbox grew from {pos_after_init} to {outbox_len}" ); - // Read position should not have advanced either (no new frames produced). - assert_eq!( - pos_after_crash, pos_after_init, - "cursor position must not advance past the initialize response" - ); } // ── Recommended test 3: oversize mock triggers FrameTooLarge ───────────── diff --git a/crates/clarion-core/src/plugin/mod.rs b/crates/clarion-core/src/plugin/mod.rs index 9f5fcf04..954d527c 100644 --- a/crates/clarion-core/src/plugin/mod.rs +++ b/crates/clarion-core/src/plugin/mod.rs @@ -8,11 +8,13 @@ //! - `limits` — Task 4: core-enforced ceilings and circuit-breakers (ADR-021 §2b–§2d). //! - `discovery` — Task 5: `$PATH` scanning for `clarion-plugin-*` executables (L9, ADR-021 §L9). //! - `host` — Task 6: plugin-host supervisor (ADR-021 §Layer 2, ADR-022, UQ-WP2-11). +//! - `host_findings` — `HostFinding` subcodes and constructors used by `host`. //! - `breaker` — Task 7: crash-loop breaker (ADR-002 + UQ-WP2-10). pub mod breaker; pub mod discovery; pub mod host; +mod host_findings; pub mod jail; pub mod limits; pub mod manifest; diff --git a/crates/clarion-core/src/plugin/protocol.rs b/crates/clarion-core/src/plugin/protocol.rs index c2bc01f7..ad474066 100644 --- a/crates/clarion-core/src/plugin/protocol.rs +++ b/crates/clarion-core/src/plugin/protocol.rs @@ -95,6 +95,11 @@ impl<'de> Deserialize<'de> for JsonRpcVersion { /// JSON-RPC 2.0 request envelope (core → plugin). /// /// Wire shape: `{"jsonrpc":"2.0","method":"...","params":{...},"id":1}` +/// +/// JSON-RPC 2.0 permits string, number, or null request IDs. Clarion narrows +/// this to `i64` as an application-level policy because the plugin transport is +/// core-initiated and core-controlled. Revisit this type before exposing the +/// envelope to external JSON-RPC peers or plugins that originate arbitrary IDs. #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)] pub struct RequestEnvelope { pub jsonrpc: JsonRpcVersion, @@ -120,6 +125,11 @@ pub struct NotificationEnvelope { /// Wire shape (success): `{"jsonrpc":"2.0","result":{...},"id":1}` /// Wire shape (error): `{"jsonrpc":"2.0","error":{...},"id":1}` /// +/// Like [`RequestEnvelope`], this intentionally accepts only `i64` IDs. That is +/// narrower than JSON-RPC 2.0 but matches Clarion's current core-issued request +/// IDs; a plugin response with a string or null ID is treated as malformed +/// plugin traffic rather than general JSON-RPC interop. +/// /// The spec (§5) requires **exactly one** of `result`/`error`. This type /// enforces that invariant during deserialisation: /// - both present → error (so a misbehaving plugin can't hide an error by @@ -140,6 +150,7 @@ pub struct ResponseEnvelope { /// Serialisation/deserialisation of the enclosing envelope is custom /// (see [`ResponseEnvelope`]) — do not add serde attributes here. #[derive(Debug, Clone, PartialEq)] +#[non_exhaustive] pub enum ResponsePayload { Result(Value), Error(ProtocolError), @@ -377,6 +388,12 @@ pub struct AnalyzeFileStats { /// Raw latency samples (milliseconds) for per-file Pyright LSP queries. #[serde(default)] pub pyright_query_latency_ms: Vec, + /// Raw latency samples (milliseconds) for Pyright-side AST index builds. + #[serde(default)] + pub pyright_index_parse_latency_ms: Vec, + /// Extractor-side `ast.parse` latency for this file in milliseconds. + #[serde(default)] + pub extractor_parse_latency_ms: u64, } impl AnalyzeFileStats { @@ -389,6 +406,8 @@ impl AnalyzeFileStats { && self.unresolved_reference_sites_total == 0 && self.unresolved_call_sites.is_empty() && self.pyright_query_latency_ms.is_empty() + && self.pyright_index_parse_latency_ms.is_empty() + && self.extractor_parse_latency_ms == 0 } } @@ -680,6 +699,8 @@ mod tests { references_skipped_cap_total: 6, unresolved_reference_sites_total: 7, pyright_query_latency_ms: vec![10, 20, 30], + pyright_index_parse_latency_ms: vec![8, 13], + extractor_parse_latency_ms: 5, }, }; let back: AnalyzeFileResult = @@ -723,6 +744,14 @@ mod tests { back.stats.pyright_query_latency_ms.is_empty(), "missing stats field must default pyright latency samples to empty" ); + assert!( + back.stats.pyright_index_parse_latency_ms.is_empty(), + "missing stats field must default pyright index parse samples to empty" + ); + assert_eq!( + back.stats.extractor_parse_latency_ms, 0, + "missing stats field must default extractor parse latency to zero" + ); // shutdown params (empty) let p = ShutdownParams {}; diff --git a/crates/clarion-core/src/plugin/transport.rs b/crates/clarion-core/src/plugin/transport.rs index 1ecfce5f..c3bab569 100644 --- a/crates/clarion-core/src/plugin/transport.rs +++ b/crates/clarion-core/src/plugin/transport.rs @@ -48,6 +48,7 @@ pub const MAX_HEADER_LINE_BYTES: usize = 8 * 1024; /// Errors that can occur during frame read/write. #[derive(Debug, Error)] +#[non_exhaustive] pub enum TransportError { /// Underlying I/O error. #[error("IO error while reading/writing frame: {0}")] diff --git a/crates/clarion-core/tests/host_subprocess.rs b/crates/clarion-core/tests/host_subprocess.rs index 249e4a8b..e8fd03f4 100644 --- a/crates/clarion-core/tests/host_subprocess.rs +++ b/crates/clarion-core/tests/host_subprocess.rs @@ -23,7 +23,8 @@ const FIXTURE_MANIFEST_BYTES: &[u8] = include_bytes!("fixtures/plugin.toml"); /// 2. `/debug/clarion-plugin-fixture` (default dev build). /// 3. `/release/clarion-plugin-fixture` (release build). /// -/// Panics with a clear message if the binary is not found. +/// Builds the fixture on demand and panics with a clear message if the binary +/// still cannot be found. fn fixture_binary_path() -> std::path::PathBuf { // Check if an explicit path was provided (e.g. by a future artifact dep). if let Ok(path) = std::env::var("CARGO_BIN_EXE_clarion-plugin-fixture") { @@ -43,21 +44,60 @@ fn fixture_binary_path() -> std::path::PathBuf { let target_dir = std::env::var("CARGO_TARGET_DIR") .map_or_else(|_| workspace_root.join("target"), std::path::PathBuf::from); - for profile in &["debug", "release"] { - let candidate = target_dir.join(profile).join("clarion-plugin-fixture"); - if candidate.exists() { - return candidate; - } + if let Some(path) = find_fixture_binary(&target_dir) { + return path; + } + + build_fixture_binary(workspace_root, &target_dir); + + if let Some(path) = find_fixture_binary(&target_dir) { + return path; } panic!( "clarion-plugin-fixture binary not found. \ - Run `cargo build -p clarion-plugin-fixture` before running this test. \ + Tried `cargo build -p clarion-plugin-fixture --bin clarion-plugin-fixture`. \ Searched in: {}", target_dir.display() ); } +fn find_fixture_binary(target_dir: &std::path::Path) -> Option { + for profile in &["debug", "release"] { + let candidate = target_dir.join(profile).join(format!( + "clarion-plugin-fixture{}", + std::env::consts::EXE_SUFFIX + )); + if candidate.exists() { + return Some(candidate); + } + } + None +} + +fn build_fixture_binary(workspace_root: &std::path::Path, target_dir: &std::path::Path) { + let cargo = std::env::var("CARGO").unwrap_or_else(|_| "cargo".to_owned()); + let output = std::process::Command::new(cargo) + .current_dir(workspace_root) + .arg("build") + .arg("-p") + .arg("clarion-plugin-fixture") + .arg("--bin") + .arg("clarion-plugin-fixture") + .arg("--target-dir") + .arg(target_dir) + .output() + .expect("spawn cargo build for clarion-plugin-fixture"); + + assert!( + output.status.success(), + "cargo build for clarion-plugin-fixture failed with status {}.\nstdout:\n{}\nstderr:\n{}", + output.status, + String::from_utf8_lossy(&output.stdout), + String::from_utf8_lossy(&output.stderr) + ); +} + /// Verify the fixture manifest parses correctly. /// This catches schema mismatches before the subprocess test runs. #[test] diff --git a/crates/clarion-mcp/Cargo.toml b/crates/clarion-mcp/Cargo.toml index b5bda014..6e17c2eb 100644 --- a/crates/clarion-mcp/Cargo.toml +++ b/crates/clarion-mcp/Cargo.toml @@ -10,6 +10,7 @@ rust-version.workspace = true workspace = true [dependencies] +blake3.workspace = true clarion-core = { path = "../clarion-core", version = "0.1.0-dev" } clarion-storage = { path = "../clarion-storage", version = "0.1.0-dev" } reqwest.workspace = true @@ -18,6 +19,7 @@ serde.workspace = true serde_json.workspace = true serde_norway.workspace = true thiserror.workspace = true +time.workspace = true tokio.workspace = true [dev-dependencies] diff --git a/crates/clarion-mcp/src/config.rs b/crates/clarion-mcp/src/config.rs index affe4057..11ab7e29 100644 --- a/crates/clarion-mcp/src/config.rs +++ b/crates/clarion-mcp/src/config.rs @@ -39,6 +39,12 @@ impl McpConfig { code: "CLA-CONFIG-DEPRECATED-PROVIDER", }); } + if self.integrations.filigree.enabled && self.integrations.filigree.actor.trim().is_empty() + { + return Err(ConfigError::InvalidFiligreeActor { + code: "CLA-CONFIG-FILIGREE-ACTOR-BLANK", + }); + } Ok(()) } } @@ -209,6 +215,9 @@ pub enum ConfigError { "{code}: llm.provider=anthropic is deprecated; use llm_policy.provider: openrouter with llm_policy.openrouter.api_key_env and llm_policy.model_id" )] DeprecatedProvider { code: &'static str }, + + #[error("{code}: integrations.filigree.actor must not be blank when Filigree is enabled")] + InvalidFiligreeActor { code: &'static str }, } #[cfg(test)] @@ -349,4 +358,19 @@ llm: assert!(err.to_string().contains("CLA-CONFIG-DEPRECATED-PROVIDER")); assert!(err.to_string().contains("provider: openrouter")); } + + #[test] + fn enabled_filigree_integration_rejects_blank_actor() { + let err = McpConfig::from_yaml_str( + r#" +integrations: + filigree: + enabled: true + actor: " " +"#, + ) + .expect_err("blank Filigree actor should be rejected"); + + assert!(err.to_string().contains("CLA-CONFIG-FILIGREE-ACTOR-BLANK")); + } } diff --git a/crates/clarion-mcp/src/lib.rs b/crates/clarion-mcp/src/lib.rs index e1b26ce7..d44f06e3 100644 --- a/crates/clarion-mcp/src/lib.rs +++ b/crates/clarion-mcp/src/lib.rs @@ -3,30 +3,31 @@ pub mod config; pub mod filigree; -use std::collections::{BTreeSet, HashMap}; +use std::collections::{BTreeSet, HashMap, HashSet}; use std::path::PathBuf; use std::sync::{Arc, Mutex}; -use std::time::{SystemTime, UNIX_EPOCH}; use clarion_core::{ EdgeConfidence, INFERRED_CALLS_PROMPT_VERSION, InferredCallsPromptInput, - LEAF_SUMMARY_PROMPT_TEMPLATE_ID, LeafSummaryPromptInput, LlmProvider, LlmPurpose, LlmRequest, - build_inferred_calls_prompt, build_leaf_summary_prompt, + LEAF_SUMMARY_PROMPT_TEMPLATE_ID, LeafSummaryPromptInput, LlmProvider, LlmProviderError, + LlmPurpose, LlmRequest, LlmResponse, build_inferred_calls_prompt, build_leaf_summary_prompt, }; use serde::{Deserialize, Serialize}; use serde_json::{Value, json}; use thiserror::Error; +use time::{Date, Month, OffsetDateTime, macros::format_description}; use tokio::sync::{Mutex as AsyncMutex, broadcast, mpsc, oneshot}; use clarion_core::plugin::{ContentLengthCeiling, Frame, TransportError}; use clarion_storage::{ CallEdgeMatch, EntityRow, InferredCallEdgeRecord, InferredEdgeCacheEntry, InferredEdgeCacheKey, - InferredEdgeWriteStats, ReaderPool, StorageError, SummaryCacheEntry, SummaryCacheKey, - UnresolvedCallSiteRow, WriterCmd, call_edges_from, call_edges_targeting, + InferredEdgeWriteStats, ReaderPool, ReferenceDirection, StorageError, SummaryCacheEntry, + SummaryCacheKey, UnresolvedCallSiteRow, WriterCmd, call_edges_from, call_edges_targeting, candidate_entities_for_unresolved_sites, child_entity_ids, contained_entity_ids, - entity_at_line, entity_by_id, find_entities, inferred_edge_cache_key_id, - inferred_edge_cache_lookup, normalize_source_path, summary_cache_lookup, - unresolved_call_sites_for_caller, unresolved_callers_for_target, + entity_at_line, entity_by_id, existing_entity_ids, find_entities, inferred_edge_cache_key_id, + inferred_edge_cache_lookup, normalize_source_path, reference_edges_for_entity, + subsystem_members, summary_cache_lookup, unresolved_call_sites_for_caller, + unresolved_callers_for_target, }; use crate::config::LlmConfig; @@ -36,6 +37,9 @@ use crate::filigree::{EntityAssociation, EntityAssociationsResponse, FiligreeLoo pub const MCP_PROTOCOL_VERSION: &str = "2025-11-25"; const EMPTY_GUIDANCE_FINGERPRINT: &str = "guidance-empty"; +type InferredInflight = + Arc>>>; + #[derive(Debug, Clone, PartialEq, Eq, Serialize)] pub struct ToolDefinition { pub name: &'static str, @@ -116,6 +120,11 @@ pub fn list_tools() -> Vec { description: "Return the one-hop Clarion neighborhood around an entity: callers, callees, container, contained entities, and references. Default confidence is resolved; ambiguous and inferred calls are opt-in. References are not execution flow.", input_schema: id_confidence_schema(), }, + ToolDefinition { + name: "subsystem_members", + description: "List module entities assigned to a subsystem entity.", + input_schema: id_schema(), + }, ] } @@ -150,6 +159,9 @@ fn id_confidence_schema() -> Value { }) } +/// Handle state-free MCP requests such as `initialize` and `tools/list`. +/// +/// Storage-backed tool calls require [`ServerState::handle_json_rpc`]. #[must_use] pub fn handle_json_rpc(request: &Value) -> Value { let id = request.get("id").cloned().unwrap_or(Value::Null); @@ -160,7 +172,11 @@ pub fn handle_json_rpc(request: &Value) -> Value { match method { "initialize" => result_response(&id, &initialize_result()), "tools/list" => result_response(&id, &json!({"tools": list_tools()})), - "tools/call" => handle_tool_call(&id, request.get("params")), + "tools/call" => error_response( + &id, + -32601, + "tools/call requires ServerState::handle_json_rpc", + ), _ => error_response(&id, -32601, "method not found"), } } @@ -172,8 +188,7 @@ pub struct ServerState { summary_llm: Option, clock: Arc String + Send + Sync>, budget: Arc>, - inferred_inflight: - Arc>>>, + inferred_inflight: InferredInflight, filigree_client: Option>, } @@ -287,6 +302,10 @@ impl ServerState { Ok(value) => value, Err(response) => return response.to_json_rpc(id), }, + "subsystem_members" => match self.tool_subsystem_members(arguments).await { + Ok(value) => value, + Err(response) => return response.to_json_rpc(id), + }, _ => unreachable!("known tools checked above"), }; @@ -450,7 +469,13 @@ impl ServerState { false, ); } - Err(err) => return tool_error_envelope("storage-error", &err.to_string(), true), + Err(err) => { + return tool_error_envelope( + "storage-error", + &err.to_string(), + storage_retryable(&err), + ); + } } let mut stats = InferredDispatchStats::default(); @@ -479,7 +504,13 @@ impl ServerState { .await { Ok(edges) => edges, - Err(err) => return tool_error_envelope("storage-error", &err.to_string(), true), + Err(err) => { + return tool_error_envelope( + "storage-error", + &err.to_string(), + storage_retryable(&err), + ); + } }; for edge in edges.into_iter().rev() { edge_count_visited += 1; @@ -515,7 +546,9 @@ impl ServerState { truncated.then_some("edge-cap"), stats.to_json(), ), - Err(err) => tool_error_envelope("storage-error", &err.to_string(), true), + Err(err) => { + tool_error_envelope("storage-error", &err.to_string(), storage_retryable(&err)) + } } } @@ -603,7 +636,13 @@ impl ServerState { "Clarion entity was not found", )); } - Err(err) => return Ok(tool_error_envelope("storage-error", &err.to_string(), true)), + Err(err) => { + return Ok(tool_error_envelope( + "storage-error", + &err.to_string(), + storage_retryable(&err), + )); + } }; let mut accumulator = IssuesForAccumulator::new(&read.entities); let mut requests_total = 0_usize; @@ -639,6 +678,52 @@ impl ServerState { Ok(accumulator.into_envelope(read.entity_cap_truncated, requests_total)) } + async fn tool_subsystem_members( + &self, + arguments: &serde_json::Map, + ) -> std::result::Result { + let subsystem_id = required_str(arguments, "id")?.to_owned(); + let result = self + .readers + .with_reader(move |conn| { + let Some(subsystem) = entity_by_id(conn, &subsystem_id)? else { + return Ok(tool_error_envelope( + "entity-not-found", + &format!("entity {subsystem_id} was not found"), + false, + )); + }; + if subsystem.kind != "subsystem" { + return Ok(tool_error_envelope( + "not-a-subsystem", + &format!("entity {} is kind {}", subsystem.id, subsystem.kind), + false, + )); + } + let members = subsystem_members(conn, &subsystem.id)? + .iter() + .map(|member| { + json!({ + "id": member.id, + "name": member.name, + "source_file_path": member.source_file_path + }) + }) + .collect::>(); + Ok(success_envelope(json!({ + "subsystem": { + "id": subsystem.id, + "name": subsystem.name, + "short_name": subsystem.short_name, + "properties": entity_properties_json(&subsystem) + }, + "members": members + }))) + }) + .await; + Ok(flatten_storage_envelope_result(result)) + } + async fn read_issues_for_entities( &self, entity_id: String, @@ -681,7 +766,13 @@ impl ServerState { .await { Ok(read) => read, - Err(err) => return Ok(tool_error_envelope("storage-error", &err.to_string(), true)), + Err(err) => { + return Ok(tool_error_envelope( + "storage-error", + &err.to_string(), + storage_retryable(&err), + )); + } }; let SummaryRead::Ready(ready) = read else { @@ -851,6 +942,7 @@ impl ServerState { &cached.result_json, self.max_inferred_edges_per_caller(), )?; + let (edges, dropped) = self.drop_unresolved_inferred_targets(edges).await?; let write = self .send_writer(&llm.writer, |ack| WriterCmd::InsertInferredEdges { cache_entry: Box::new(cached), @@ -859,7 +951,9 @@ impl ServerState { }) .await .map_err(|err| InferredDispatchFailure::from_storage(&err))?; - Ok(InferredDispatchStats::cache_hit(write)) + let mut stats = InferredDispatchStats::cache_hit(write); + stats.unresolved_targets_dropped_total = dropped; + Ok(stats) } async fn coalesced_inferred_dispatch( @@ -868,14 +962,14 @@ impl ServerState { read: InferredRead, llm: InferenceLlmState, ) -> Result { - let maybe_rx = { + let (maybe_rx, leader_sender) = { let mut in_flight = self.inferred_inflight.lock().await; if let Some(sender) = in_flight.get(&key) { - Some(sender.subscribe()) + (Some(sender.subscribe()), None) } else { let (sender, _) = broadcast::channel(8); - in_flight.insert(key.clone(), sender); - None + in_flight.insert(key.clone(), sender.clone()); + (None, Some(sender)) } }; @@ -899,9 +993,14 @@ impl ServerState { }; } + let guard = InferredInflightGuard::new( + Arc::clone(&self.inferred_inflight), + key, + leader_sender.expect("leader sender is present for non-coalesced dispatch"), + ); let outcome = InferredDispatchOutcome::from_result(self.perform_inferred_dispatch(read, &llm).await); - if let Some(sender) = self.inferred_inflight.lock().await.remove(&key) { + if let Some(sender) = guard.remove().await { let _ = sender.send(outcome.clone()); } outcome.into_result() @@ -912,18 +1011,21 @@ impl ServerState { read: InferredRead, llm: &InferenceLlmState, ) -> Result { + let caller_source_excerpt = + verified_source_excerpt(&read.caller).map_err(|err| err.to_inferred_failure())?; let prompt = build_inferred_calls_prompt(&InferredCallsPromptInput { caller_entity_id: read.caller.id.clone(), - caller_source_excerpt: source_excerpt(&read.caller), + caller_source_excerpt, unresolved_call_sites_json: unresolved_sites_json(&read.sites), candidate_entities_json: entities_json(&read.candidates), + max_edges: self.max_inferred_edges_per_caller(), }); let request = LlmRequest { purpose: LlmPurpose::InferredEdges, model_id: read.key.model_id.clone(), prompt_id: prompt.id.to_owned(), prompt: prompt.body, - max_output_tokens: 512, + max_output_tokens: 2048, }; let Some(reservation) = self.reserve_budget( llm.provider.estimate_tokens(&request), @@ -935,9 +1037,15 @@ impl ServerState { false, )); }; - let response = llm.provider.invoke(request).map_err(|err| { - InferredDispatchFailure::new("llm-provider-error", &err.to_string(), err.retryable()) - })?; + let response = invoke_llm_provider(Arc::clone(&llm.provider), request) + .await + .map_err(|err| { + InferredDispatchFailure::new( + "llm-provider-error", + &err.to_string(), + err.retryable(), + ) + })?; if !reservation.commit( u64::from(response.total_tokens), llm.config.session_token_ceiling, @@ -948,15 +1056,30 @@ impl ServerState { false, )); } - let edges = inferred_records_from_result( + let edges = match inferred_records_from_result( &read, &response.output_json, self.max_inferred_edges_per_caller(), - )?; + ) { + Ok(edges) => edges, + Err(err) if err.code == "llm-invalid-json" => { + let message = err.message.clone(); + return Err(err.with_stats( + inferred_usage_stats(&response, true), + vec![json!({ + "code": "CLA-LLM-INVALID-JSON", + "message": message, + "usage": llm_usage_json(&response) + })], + )); + } + Err(err) => return Err(err), + }; + let (edges, dropped) = self.drop_unresolved_inferred_targets(edges).await?; let now = (self.clock)(); let entry = InferredEdgeCacheEntry { key: read.key, - result_json: response.output_json, + result_json: response.output_json.clone(), cost_usd: response.cost_usd, token_count: i64::from(response.total_tokens), created_at: now.clone(), @@ -970,7 +1093,44 @@ impl ServerState { }) .await .map_err(|err| InferredDispatchFailure::from_storage(&err))?; - Ok(InferredDispatchStats::cache_miss(write, entry.token_count)) + let mut stats = InferredDispatchStats::cache_miss(write, &response); + stats.unresolved_targets_dropped_total = dropped; + Ok(stats) + } + + /// Strip `to_id`s that don't exist in the `entities` table so the + /// writer-actor's FK-protected INSERT never sees a hallucinated edge + /// target (clarion-df58379de4). Returns the surviving records and the + /// count of dropped edges so callers can fold the number into + /// `InferredDispatchStats`. + async fn drop_unresolved_inferred_targets( + &self, + records: Vec, + ) -> Result<(Vec, u64), InferredDispatchFailure> { + if records.is_empty() { + return Ok((records, 0)); + } + let unique_targets: Vec = records + .iter() + .map(|record| record.to_id.clone()) + .collect::>() + .into_iter() + .collect(); + let existing = self + .readers + .with_reader({ + let targets = unique_targets.clone(); + move |conn| existing_entity_ids(conn, &targets) + }) + .await + .map_err(|err| InferredDispatchFailure::from_storage(&err))?; + let original_len = records.len(); + let kept: Vec = records + .into_iter() + .filter(|record| existing.contains(&record.to_id)) + .collect(); + let dropped = u64::try_from(original_len - kept.len()).unwrap_or(0); + Ok((kept, dropped)) } async fn read_summary_inputs( @@ -983,6 +1143,9 @@ impl ServerState { let Some(entity) = entity_by_id(conn, &entity_id)? else { return Ok(SummaryRead::EntityNotFound(entity_id)); }; + if entity.kind == "subsystem" { + return Ok(SummaryRead::ScopeDeferred(Box::new(entity))); + } let Some(content_hash) = entity.content_hash.clone() else { return Ok(SummaryRead::MissingContentHash(entity.id)); }; @@ -1027,7 +1190,11 @@ impl ServerState { }) .await { - return Some(tool_error_envelope("storage-error", &err.to_string(), true)); + return Some(tool_error_envelope( + "storage-error", + &err.to_string(), + storage_retryable(&err), + )); } Some(summary_success_envelope( &ready.entity, @@ -1045,11 +1212,15 @@ impl ServerState { now: String, ) -> Value { let model_id = self.summary_model_id(); + let source_excerpt = match verified_source_excerpt(&ready.entity) { + Ok(excerpt) => excerpt, + Err(err) => return err.to_envelope(), + }; let prompt = build_leaf_summary_prompt(&LeafSummaryPromptInput { entity_id: ready.entity.id.clone(), kind: ready.entity.kind.clone(), name: ready.entity.name.clone(), - source_excerpt: source_excerpt(&ready.entity), + source_excerpt, }); let request = LlmRequest { purpose: LlmPurpose::Summary, @@ -1064,7 +1235,7 @@ impl ServerState { ) else { return token_ceiling_envelope("LLM session token ceiling has been reached"); }; - let response = match summary_llm.provider.invoke(request) { + let response = match invoke_llm_provider(Arc::clone(&summary_llm.provider), request).await { Ok(response) => response, Err(err) => { return tool_error_envelope( @@ -1083,10 +1254,16 @@ impl ServerState { } if serde_json::from_str::(&response.output_json).is_err() { - return tool_error_envelope( + return tool_error_envelope_with_diagnostics( "llm-invalid-json", "summary provider returned non-JSON output", true, + summary_usage_stats(&response, true), + vec![json!({ + "code": "CLA-LLM-INVALID-JSON", + "message": "summary provider returned non-JSON output", + "usage": llm_usage_json(&response) + })], ); } @@ -1109,7 +1286,7 @@ impl ServerState { }) .await { - return tool_error_envelope("storage-error", &err.to_string(), true); + return tool_error_envelope("storage-error", &err.to_string(), storage_retryable(&err)); } summary_success_envelope( @@ -1121,7 +1298,8 @@ impl ServerState { "summary_cache_misses_total": 1, "summary_tokens_input": entry.tokens_input, "summary_tokens_output": entry.tokens_output, - "summary_tokens_total": entry.tokens_input + entry.tokens_output + "summary_tokens_total": entry.tokens_input + entry.tokens_output, + "summary_cost_usd": entry.cost_usd }), ) } @@ -1223,6 +1401,18 @@ impl ServerState { } } +async fn invoke_llm_provider( + provider: Arc, + request: LlmRequest, +) -> Result { + tokio::task::spawn_blocking(move || provider.invoke(request)) + .await + .map_err(|err| LlmProviderError::InvalidResponse { + message: format!("LLM provider task failed: {err}"), + retryable: true, + })? +} + struct SummaryLlmState { writer: mpsc::Sender, config: LlmConfig, @@ -1252,7 +1442,10 @@ impl BudgetReservation { budget.reserved_tokens = budget.reserved_tokens.saturating_sub(self.amount_tokens); self.active = false; } - if budget.blocked || budget.spent_tokens.saturating_add(actual_tokens) > ceiling_tokens { + // `budget.blocked` gates *new* reservations, not in-flight commits. + // A reservation that already cleared reserve_budget paid for its + // dispatch slot; commit it iff the actual usage fits the ceiling. + if budget.spent_tokens.saturating_add(actual_tokens) > ceiling_tokens { budget.blocked = true; return false; } @@ -1279,6 +1472,7 @@ enum SummaryRead { Ready(Box), EntityNotFound(String), MissingContentHash(String), + ScopeDeferred(Box), } struct SummaryReady { @@ -1405,6 +1599,71 @@ struct InferenceLlmState { provider: Arc, } +struct InferredInflightGuard { + in_flight: InferredInflight, + key: InferredEdgeCacheKey, + sender: broadcast::Sender, + active: bool, +} + +impl InferredInflightGuard { + fn new( + in_flight: InferredInflight, + key: InferredEdgeCacheKey, + sender: broadcast::Sender, + ) -> Self { + Self { + in_flight, + key, + sender, + active: true, + } + } + + async fn remove(mut self) -> Option> { + let removed = remove_matching_inferred_inflight( + Arc::clone(&self.in_flight), + self.key.clone(), + self.sender.clone(), + ) + .await; + self.active = false; + removed + } +} + +impl Drop for InferredInflightGuard { + fn drop(&mut self) { + if !self.active { + return; + } + let in_flight = Arc::clone(&self.in_flight); + let key = self.key.clone(); + let sender = self.sender.clone(); + if let Ok(handle) = tokio::runtime::Handle::try_current() { + handle.spawn(async move { + let _ = remove_matching_inferred_inflight(in_flight, key, sender).await; + }); + } + } +} + +async fn remove_matching_inferred_inflight( + in_flight: InferredInflight, + key: InferredEdgeCacheKey, + sender: broadcast::Sender, +) -> Option> { + let mut map = in_flight.lock().await; + if map + .get(&key) + .is_some_and(|current| current.same_channel(&sender)) + { + map.remove(&key) + } else { + None + } +} + #[derive(Clone)] struct InferredRead { caller: EntityRow, @@ -1420,9 +1679,17 @@ struct InferredDispatchStats { cache_misses_total: u64, edges_materialized_total: u64, edges_skipped_static_duplicates_total: u64, + /// LLM-proposed `to_id` values that did not resolve in the `entities` + /// table at write time (clarion-df58379de4). Counted here, dropped from + /// the persisted edge set to avoid the FK violation that previously + /// poisoned the cache row and re-burned LLM tokens on retry. + unresolved_targets_dropped_total: u64, candidate_callers_considered: u64, coalesced_waits_total: u64, + tokens_input: i64, + tokens_output: i64, tokens_total: i64, + cost_usd: f64, } impl InferredDispatchStats { @@ -1435,12 +1702,15 @@ impl InferredDispatchStats { } } - fn cache_miss(write: InferredEdgeWriteStats, tokens: i64) -> Self { + fn cache_miss(write: InferredEdgeWriteStats, response: &LlmResponse) -> Self { Self { cache_misses_total: 1, edges_materialized_total: write.inserted_edges, edges_skipped_static_duplicates_total: write.skipped_static_duplicates, - tokens_total: tokens, + tokens_input: i64::from(response.input_tokens), + tokens_output: i64::from(response.output_tokens), + tokens_total: i64::from(response.total_tokens), + cost_usd: response.cost_usd, ..Self::default() } } @@ -1450,9 +1720,13 @@ impl InferredDispatchStats { self.cache_misses_total += other.cache_misses_total; self.edges_materialized_total += other.edges_materialized_total; self.edges_skipped_static_duplicates_total += other.edges_skipped_static_duplicates_total; + self.unresolved_targets_dropped_total += other.unresolved_targets_dropped_total; self.candidate_callers_considered += other.candidate_callers_considered; self.coalesced_waits_total += other.coalesced_waits_total; + self.tokens_input += other.tokens_input; + self.tokens_output += other.tokens_output; self.tokens_total += other.tokens_total; + self.cost_usd += other.cost_usd; } fn to_json(&self) -> Value { @@ -1461,9 +1735,13 @@ impl InferredDispatchStats { "inferred_dispatch_misses_total": self.cache_misses_total, "inferred_edges_materialized_total": self.edges_materialized_total, "inferred_edges_skipped_static_duplicates_total": self.edges_skipped_static_duplicates_total, + "inferred_unresolved_targets_dropped_total": self.unresolved_targets_dropped_total, "inferred_candidate_callers_considered": self.candidate_callers_considered, "inferred_dispatch_coalesced_total": self.coalesced_waits_total, - "inferred_tokens_total": self.tokens_total + "inferred_tokens_input": self.tokens_input, + "inferred_tokens_output": self.tokens_output, + "inferred_tokens_total": self.tokens_total, + "inferred_cost_usd": self.cost_usd }) } } @@ -1473,6 +1751,8 @@ struct InferredDispatchFailure { code: &'static str, message: String, retryable: bool, + stats_delta: Value, + diagnostics: Vec, } impl InferredDispatchFailure { @@ -1481,22 +1761,42 @@ impl InferredDispatchFailure { code, message: message.to_owned(), retryable, + stats_delta: json!({}), + diagnostics: Vec::new(), } } fn from_storage(err: &StorageError) -> Self { + // FK violations are deterministic against the same row set; treating + // them as `retryable=true` causes the client to re-issue the LLM call + // and re-pay the token cost (clarion-df58379de4). Mark them + // non-retryable so a client honouring the hint gives up immediately. Self { code: "storage-error", message: err.to_string(), - retryable: true, + retryable: !err.is_foreign_key_violation(), + stats_delta: json!({}), + diagnostics: Vec::new(), } } + fn with_stats(mut self, stats_delta: Value, diagnostics: Vec) -> Self { + self.stats_delta = stats_delta; + self.diagnostics = diagnostics; + self + } + fn to_envelope(&self) -> Value { if self.code == "token-ceiling-exceeded" { return token_ceiling_envelope(&self.message); } - tool_error_envelope(self.code, &self.message, self.retryable) + tool_error_envelope_with_diagnostics( + self.code, + &self.message, + self.retryable, + self.stats_delta.clone(), + self.diagnostics.clone(), + ) } } @@ -1548,6 +1848,9 @@ pub enum McpError { Runtime(#[from] std::io::Error), } +/// Decode and handle a state-free MCP frame. +/// +/// Storage-backed tool calls require [`handle_frame_with_state`]. pub fn handle_frame(frame: &Frame) -> Result { let request = serde_json::from_slice(&frame.body)?; let response = handle_json_rpc(&request); @@ -1567,6 +1870,9 @@ pub async fn handle_frame_with_state( }) } +/// Serve state-free MCP protocol metadata over stdio. +/// +/// Storage-backed tool calls require [`serve_stdio_with_state`]. pub fn serve_stdio( reader: &mut impl std::io::BufRead, writer: &mut impl std::io::Write, @@ -1628,43 +1934,6 @@ fn initialize_result() -> Value { }) } -fn handle_tool_call(id: &Value, params: Option<&Value>) -> Value { - let Some(params) = params.and_then(Value::as_object) else { - return error_response(id, -32602, "invalid tools/call params"); - }; - let Some(name) = params.get("name").and_then(Value::as_str) else { - return error_response(id, -32602, "invalid tools/call params: missing name"); - }; - if !list_tools().iter().any(|tool| tool.name == name) { - return error_response(id, -32601, &format!("unknown tool: {name}")); - } - - result_response( - id, - &json!({ - "content": [ - { - "type": "text", - "text": serde_json::to_string(&json!({ - "ok": false, - "result": null, - "error": { - "code": "tool-unimplemented", - "message": format!("{name} is not implemented yet"), - "retryable": false - }, - "diagnostics": [], - "truncated": false, - "truncation_reason": null, - "stats_delta": {} - })).expect("tool error envelope serializes") - } - ], - "isError": true - }), - ) -} - #[derive(Debug)] struct ParamError { message: String, @@ -1731,12 +2000,6 @@ impl PathTraversal { } } -#[derive(Clone, Copy)] -enum ReferenceDirection { - In, - Out, -} - fn required_str<'a>( arguments: &'a serde_json::Map, field: &str, @@ -1804,17 +2067,24 @@ fn optional_confidence( fn envelope_from_storage_result(result: Result) -> Value { match result { Ok(result) => success_envelope(result), - Err(err) => tool_error_envelope("storage-error", &err.to_string(), true), + Err(err) => tool_error_envelope("storage-error", &err.to_string(), storage_retryable(&err)), } } fn flatten_storage_envelope_result(result: Result) -> Value { match result { Ok(envelope) => envelope, - Err(err) => tool_error_envelope("storage-error", &err.to_string(), true), + Err(err) => tool_error_envelope("storage-error", &err.to_string(), storage_retryable(&err)), } } +/// `storage-error` retryable hint. FK violations are deterministic against +/// the same row set; everything else (`SQLITE_BUSY`, disk-full, pool errors) +/// stays retryable (clarion-df58379de4). +fn storage_retryable(err: &StorageError) -> bool { + !err.is_foreign_key_violation() +} + fn success_envelope(result: Value) -> Value { success_envelope_with_truncation(result, None) } @@ -1858,21 +2128,87 @@ fn success_envelope_with_stats(result: Value, stats_delta: Value) -> Value { } fn tool_error_envelope(code: &str, message: &str, retryable: bool) -> Value { - json!({ - "ok": false, - "result": null, - "error": { + tool_error_envelope_with_diagnostics(code, message, retryable, json!({}), Vec::new()) +} + +fn tool_error_envelope_with_diagnostics( + code: &str, + message: &str, + retryable: bool, + stats_delta: Value, + diagnostics: Vec, +) -> Value { + let mut envelope = serde_json::Map::new(); + envelope.insert("ok".to_owned(), Value::Bool(false)); + envelope.insert("result".to_owned(), Value::Null); + envelope.insert( + "error".to_owned(), + json!({ "code": code, "message": message, - "retryable": retryable - }, - "diagnostics": [], - "truncated": false, - "truncation_reason": null, - "stats_delta": {} + "retryable": retryable, + }), + ); + envelope.insert("diagnostics".to_owned(), Value::Array(diagnostics)); + envelope.insert("truncated".to_owned(), Value::Bool(false)); + envelope.insert("truncation_reason".to_owned(), Value::Null); + envelope.insert("stats_delta".to_owned(), stats_delta); + Value::Object(envelope) +} + +fn llm_usage_json(response: &LlmResponse) -> Value { + json!({ + "tokens_input": response.input_tokens, + "tokens_output": response.output_tokens, + "tokens_total": response.total_tokens, + "cost_usd": response.cost_usd }) } +fn summary_usage_stats(response: &LlmResponse, invalid_json: bool) -> Value { + let mut stats = serde_json::Map::new(); + stats.insert("summary_cache_misses_total".to_owned(), json!(1)); + stats.insert( + "summary_tokens_input".to_owned(), + json!(response.input_tokens), + ); + stats.insert( + "summary_tokens_output".to_owned(), + json!(response.output_tokens), + ); + stats.insert( + "summary_tokens_total".to_owned(), + json!(response.total_tokens), + ); + stats.insert("summary_cost_usd".to_owned(), json!(response.cost_usd)); + if invalid_json { + stats.insert("llm_invalid_json_total".to_owned(), json!(1)); + } + Value::Object(stats) +} + +fn inferred_usage_stats(response: &LlmResponse, invalid_json: bool) -> Value { + let mut stats = serde_json::Map::new(); + stats.insert("inferred_dispatch_misses_total".to_owned(), json!(1)); + stats.insert( + "inferred_tokens_input".to_owned(), + json!(response.input_tokens), + ); + stats.insert( + "inferred_tokens_output".to_owned(), + json!(response.output_tokens), + ); + stats.insert( + "inferred_tokens_total".to_owned(), + json!(response.total_tokens), + ); + stats.insert("inferred_cost_usd".to_owned(), json!(response.cost_usd)); + if invalid_json { + stats.insert("llm_invalid_json_total".to_owned(), json!(1)); + } + Value::Object(stats) +} + fn token_ceiling_envelope(message: &str) -> Value { json!({ "ok": false, @@ -1937,10 +2273,35 @@ fn summary_read_error(read: SummaryRead) -> Value { &format!("entity {id} has no content hash for summary cache keying"), false, ), + SummaryRead::ScopeDeferred(entity) => summary_scope_deferred(&entity), SummaryRead::Ready(_) => unreachable!("ready summary read is not an error"), } } +#[derive(Debug)] +struct SourceExcerptError { + entity_id: String, + stored_content_hash: String, + current_content_hash: String, +} + +impl SourceExcerptError { + fn message(&self) -> String { + format!( + "entity {} source content drifted: stored content_hash {} but current file hashes to {}; rerun `clarion analyze` before requesting LLM output", + self.entity_id, self.stored_content_hash, self.current_content_hash + ) + } + + fn to_envelope(&self) -> Value { + tool_error_envelope("content-drift", &self.message(), false) + } + + fn to_inferred_failure(&self) -> InferredDispatchFailure { + InferredDispatchFailure::new("content-drift", &self.message(), false) + } +} + fn summary_success_envelope( entity: &EntityRow, entry: &SummaryCacheEntry, @@ -1977,6 +2338,15 @@ fn summary_success_envelope( ) } +fn summary_scope_deferred(entity: &EntityRow) -> Value { + success_envelope(json!({ + "available": false, + "reason": "summary-scope-deferred", + "message": "subsystem summaries are deferred to v0.2", + "entity": entity_json(entity) + })) +} + fn tool_json_rpc_response(id: &Value, envelope: &Value) -> Value { let is_error = !envelope .get("ok") @@ -2009,18 +2379,61 @@ fn entity_json(entity: &EntityRow) -> Value { }) } -fn source_excerpt(entity: &EntityRow) -> String { - entity - .source_file_path - .as_deref() - .and_then(|path| std::fs::read_to_string(path).ok()) - .map(|source| { - let excerpt = - line_range_excerpt(&source, entity.source_line_start, entity.source_line_end) - .unwrap_or(source); - truncate_excerpt(excerpt) - }) - .unwrap_or_default() +fn entity_properties_json(entity: &EntityRow) -> Value { + serde_json::from_str::(&entity.properties_json) + .expect("entity properties_json should be valid JSON") +} + +fn verified_source_excerpt(entity: &EntityRow) -> Result { + let Some(path) = entity.source_file_path.as_deref() else { + return Ok(String::new()); + }; + let Ok(bytes) = std::fs::read(path) else { + return Ok(String::new()); + }; + let source = String::from_utf8(bytes.clone()).ok(); + if let (Some(stored_content_hash), Some(current_content_hash)) = ( + entity.content_hash.as_deref(), + current_source_content_hash(entity, &bytes, source.as_deref()), + ) && stored_content_hash != current_content_hash + { + return Err(SourceExcerptError { + entity_id: entity.id.clone(), + stored_content_hash: stored_content_hash.to_owned(), + current_content_hash, + }); + } + let Some(source) = source else { + return Ok(String::new()); + }; + let excerpt = line_range_excerpt(&source, entity.source_line_start, entity.source_line_end) + .unwrap_or(source); + Ok(truncate_excerpt(excerpt)) +} + +fn current_source_content_hash( + entity: &EntityRow, + file_bytes: &[u8], + source: Option<&str>, +) -> Option { + if entity.kind == "module" { + return Some(blake3::hash(file_bytes).to_hex().to_string()); + } + let source = source?; + let start_line = entity.source_line_start?; + let end_line = entity.source_line_end?; + if start_line <= 0 || end_line < start_line { + return None; + } + let start = usize::try_from(start_line - 1).ok()?; + let mut end = usize::try_from(end_line).ok()?; + let lines = source.lines().collect::>(); + end = end.min(lines.len()); + if start >= end { + return None; + } + let normalized = lines[start..end].join("\n"); + Some(blake3::hash(normalized.as_bytes()).to_hex().to_string()) } fn line_range_excerpt( @@ -2160,27 +2573,14 @@ fn timestamp_day_index(raw: &str) -> Option { return seconds.parse::().ok().map(|value| value / 86_400); } let date = raw.get(..10)?; - let mut parts = date.split('-'); - let year = parts.next()?.parse::().ok()?; - let month = parts.next()?.parse::().ok()?; - let day = parts.next()?.parse::().ok()?; - Some(days_from_civil(year, month, day)) -} - -fn days_from_civil(year: i64, month: i64, day: i64) -> i64 { - let year = year - i64::from(month <= 2); - let era = if year >= 0 { year } else { year - 399 } / 400; - let yoe = year - era * 400; - let month_prime = month + if month > 2 { -3 } else { 9 }; - let doy = (153 * month_prime + 2) / 5 + day - 1; - let doe = yoe * 365 + yoe / 4 - yoe / 100 + doy; - era * 146_097 + doe - 719_468 + let date = Date::parse(date, format_description!("[year]-[month]-[day]")).ok()?; + let unix_epoch = Date::from_calendar_date(1970, Month::January, 1) + .expect("Unix epoch is a valid calendar date"); + Some(i64::from(date.to_julian_day() - unix_epoch.to_julian_day())) } fn default_now_string() -> String { - let seconds = SystemTime::now() - .duration_since(UNIX_EPOCH) - .map_or(0, |duration| duration.as_secs()); + let seconds = OffsetDateTime::now_utc().unix_timestamp(); format!("unix:{seconds}") } @@ -2229,34 +2629,14 @@ fn reference_neighbors( entity_id: &str, direction: ReferenceDirection, ) -> Result, StorageError> { - let (predicate, neighbor_column) = match direction { - ReferenceDirection::In => ("to_id = ?1", "from_id"), - ReferenceDirection::Out => ("from_id = ?1", "to_id"), - }; - let sql = format!( - "SELECT {neighbor_column}, confidence, source_byte_start, source_byte_end \ - FROM edges \ - WHERE kind = 'references' AND {predicate} \ - ORDER BY {neighbor_column}, source_byte_start, source_byte_end" - ); - let mut stmt = conn.prepare(&sql)?; - let rows = stmt.query_map(rusqlite::params![entity_id], |row| { - Ok(( - row.get::<_, String>(0)?, - row.get::<_, String>(1)?, - row.get::<_, Option>(2)?, - row.get::<_, Option>(3)?, - )) - })?; let mut neighbors = Vec::new(); - for row in rows { - let (neighbor_id, confidence, source_byte_start, source_byte_end) = row?; - if let Some(entity) = entity_by_id(conn, &neighbor_id)? { + for edge in reference_edges_for_entity(conn, entity_id, direction)? { + if let Some(entity) = entity_by_id(conn, &edge.neighbor_id)? { neighbors.push(json!({ "entity": entity_json(&entity), - "edge_confidence": confidence, - "source_byte_start": source_byte_start, - "source_byte_end": source_byte_end + "edge_confidence": edge.confidence.as_str(), + "source_byte_start": edge.source_byte_start, + "source_byte_end": edge.source_byte_end })); } } @@ -2284,13 +2664,23 @@ fn error_response(id: &Value, code: i64, message: &str) -> Value { #[cfg(test)] mod tests { - use super::list_tools; + use std::sync::{Arc, Mutex}; + use std::time::Duration; + + use clarion_core::{CachingModel, LlmProvider, LlmProviderError, LlmRequest, LlmResponse}; + use clarion_storage::{ + EntityRow, InferredEdgeCacheKey, ReaderPool, UnresolvedCallSiteRow, pragma, schema, + }; + use rusqlite::Connection; + use tokio::sync::mpsc; + + use super::{InferenceLlmState, InferredRead, ServerState, config::LlmConfig, list_tools}; #[test] fn tools_list_exposes_exact_docstrings() { let tools = list_tools(); - assert_eq!(tools.len(), 7); + assert_eq!(tools.len(), 8); assert_eq!(tools[0].name, "entity_at"); assert_eq!( tools[0].description, @@ -2326,6 +2716,11 @@ mod tests { tools[6].description, "Return the one-hop Clarion neighborhood around an entity: callers, callees, container, contained entities, and references. Default confidence is resolved; ambiguous and inferred calls are opt-in. References are not execution flow." ); + assert_eq!(tools[7].name, "subsystem_members"); + assert_eq!( + tools[7].description, + "List module entities assigned to a subsystem entity." + ); } #[test] @@ -2362,8 +2757,9 @@ mod tests { assert_eq!(response["jsonrpc"], "2.0"); assert_eq!(response["id"], "tools-1"); - assert_eq!(response["result"]["tools"].as_array().unwrap().len(), 7); + assert_eq!(response["result"]["tools"].as_array().unwrap().len(), 8); assert_eq!(response["result"]["tools"][0]["name"], "entity_at"); + assert_eq!(response["result"]["tools"][7]["name"], "subsystem_members"); } #[test] @@ -2379,7 +2775,7 @@ mod tests { } #[test] - fn call_tool_rejects_unknown_tool() { + fn stateless_call_tool_requires_server_state_before_tool_validation() { let response = super::handle_json_rpc(&serde_json::json!({ "jsonrpc": "2.0", "id": 8, @@ -2388,11 +2784,32 @@ mod tests { })); assert_eq!(response["error"]["code"], -32601); - assert_eq!(response["error"]["message"], "unknown tool: not_a_tool"); + assert_eq!( + response["error"]["message"], + "tools/call requires ServerState::handle_json_rpc" + ); } #[test] - fn call_tool_rejects_invalid_params() { + fn stateless_json_rpc_does_not_fake_tool_calls() { + let response = super::handle_json_rpc(&serde_json::json!({ + "jsonrpc": "2.0", + "id": 88, + "method": "tools/call", + "params": {"name": "summary", "arguments": {"id": "python:function:demo.entry"}} + })); + + assert_eq!(response["error"]["code"], -32601); + assert!( + response["error"]["message"] + .as_str() + .unwrap() + .contains("ServerState") + ); + } + + #[test] + fn stateless_call_tool_with_invalid_params_requires_server_state() { let response = super::handle_json_rpc(&serde_json::json!({ "jsonrpc": "2.0", "id": 9, @@ -2400,7 +2817,11 @@ mod tests { "params": {"arguments": {}} })); - assert_eq!(response["error"]["code"], -32602); + assert_eq!(response["error"]["code"], -32601); + assert_eq!( + response["error"]["message"], + "tools/call requires ServerState::handle_json_rpc" + ); } #[test] @@ -2420,7 +2841,7 @@ mod tests { assert_eq!(decoded["jsonrpc"], "2.0"); assert_eq!(decoded["id"], 10); - assert_eq!(decoded["result"]["tools"].as_array().unwrap().len(), 7); + assert_eq!(decoded["result"]["tools"].as_array().unwrap().len(), 8); } #[test] @@ -2479,6 +2900,162 @@ mod tests { assert_eq!(first_json["id"], 11); assert_eq!(first_json["result"]["serverInfo"]["name"], "clarion"); assert_eq!(second_json["id"], 12); - assert_eq!(second_json["result"]["tools"].as_array().unwrap().len(), 7); + assert_eq!(second_json["result"]["tools"].as_array().unwrap().len(), 8); + } + + #[tokio::test] + async fn inferred_inflight_entry_is_removed_when_leader_future_is_aborted() { + let project = tempfile::tempdir().expect("temp project"); + let db_path = project.path().join("clarion.db"); + let mut conn = Connection::open(&db_path).expect("open sqlite"); + pragma::apply_write_pragmas(&conn).expect("write pragmas"); + schema::apply_migrations(&mut conn).expect("apply migrations"); + drop(conn); + + let readers = ReaderPool::open(&db_path, 1).expect("reader pool"); + let state = Arc::new(ServerState::new(project.path().to_path_buf(), readers)); + let key = inferred_test_key(); + let read = inferred_test_read(key.clone()); + let (writer, _rx) = mpsc::channel(1); + let (release_tx, release_rx) = std::sync::mpsc::channel(); + let llm = InferenceLlmState { + writer, + config: LlmConfig::default(), + provider: Arc::new(BlockingProvider { + release: Mutex::new(release_rx), + }), + }; + + let leader_state = Arc::clone(&state); + let leader_key = key.clone(); + let handle = tokio::spawn(async move { + leader_state + .coalesced_inferred_dispatch(leader_key, read, llm) + .await + }); + assert_inferred_inflight_contains(&state, &key).await; + + handle.abort(); + let _ = handle.await; + let removed = wait_until_inferred_inflight_removed(&state, &key).await; + let _ = release_tx.send(()); + + assert!( + removed, + "aborted inferred-dispatch leader left stale in-flight key" + ); + } + + async fn assert_inferred_inflight_contains(state: &ServerState, key: &InferredEdgeCacheKey) { + for _ in 0..50 { + if state.inferred_inflight.lock().await.contains_key(key) { + return; + } + tokio::time::sleep(Duration::from_millis(10)).await; + } + panic!("inferred-dispatch leader never registered in-flight key"); + } + + async fn wait_until_inferred_inflight_removed( + state: &ServerState, + key: &InferredEdgeCacheKey, + ) -> bool { + for _ in 0..50 { + if !state.inferred_inflight.lock().await.contains_key(key) { + return true; + } + tokio::time::sleep(Duration::from_millis(10)).await; + } + false + } + + fn inferred_test_key() -> InferredEdgeCacheKey { + InferredEdgeCacheKey { + caller_entity_id: "python:function:demo.dynamic".to_owned(), + caller_content_hash: "hash-caller".to_owned(), + model_id: "test-model".to_owned(), + prompt_version: "test-prompt".to_owned(), + } + } + + fn inferred_test_read(key: InferredEdgeCacheKey) -> InferredRead { + InferredRead { + caller: entity_row(&key.caller_entity_id, "dynamic", Some("hash-caller")), + sites: vec![UnresolvedCallSiteRow { + caller_entity_id: key.caller_entity_id.clone(), + caller_content_hash: key.caller_content_hash.clone(), + site_key: "site-1".to_owned(), + site_ordinal: 0, + source_file_id: Some("python:module:demo".to_owned()), + source_byte_start: 0, + source_byte_end: 8, + callee_expr: "target()".to_owned(), + }], + candidates: vec![entity_row( + "python:function:demo.target", + "target", + Some("hash-target"), + )], + key, + cached: None, + } + } + + fn entity_row(id: &str, name: &str, content_hash: Option<&str>) -> EntityRow { + EntityRow { + id: id.to_owned(), + plugin_id: "python".to_owned(), + kind: "function".to_owned(), + name: name.to_owned(), + short_name: name.to_owned(), + parent_id: Some("python:module:demo".to_owned()), + source_file_id: Some("python:module:demo".to_owned()), + source_file_path: None, + source_byte_start: Some(0), + source_byte_end: Some(8), + source_line_start: Some(1), + source_line_end: Some(1), + properties_json: "{}".to_owned(), + content_hash: content_hash.map(str::to_owned), + summary_json: None, + } + } + + struct BlockingProvider { + release: Mutex>, + } + + impl LlmProvider for BlockingProvider { + fn name(&self) -> &'static str { + "blocking" + } + + fn invoke(&self, _request: LlmRequest) -> Result { + let _ = self + .release + .lock() + .unwrap_or_else(std::sync::PoisonError::into_inner) + .recv(); + Ok(LlmResponse { + model_id: "test-model".to_owned(), + output_json: r#"{"edges":[]}"#.to_owned(), + input_tokens: 1, + output_tokens: 1, + total_tokens: 2, + cost_usd: 0.0, + }) + } + + fn estimate_tokens(&self, _request: &LlmRequest) -> u64 { + 1 + } + + fn tier_to_model(&self, _tier: &str) -> Option<&str> { + Some("test-model") + } + + fn caching_model(&self) -> CachingModel { + CachingModel::OpenAiChatCompletions + } } } diff --git a/crates/clarion-mcp/tests/storage_tools.rs b/crates/clarion-mcp/tests/storage_tools.rs index 383c6c6b..02519070 100644 --- a/crates/clarion-mcp/tests/storage_tools.rs +++ b/crates/clarion-mcp/tests/storage_tools.rs @@ -1,12 +1,15 @@ //! MCP storage-backed tool tests. -use std::sync::{Arc, Mutex}; +use std::{ + fs, + sync::{Arc, Mutex}, +}; use clarion_core::{ CachingModel, INFERRED_CALLS_PROMPT_VERSION, InferredCallsPromptInput, LEAF_SUMMARY_PROMPT_TEMPLATE_ID, LeafSummaryPromptInput, LlmProvider, LlmProviderError, - LlmPurpose, LlmRequest, LlmResponse, Recording, RecordingProvider, build_inferred_calls_prompt, - build_leaf_summary_prompt, + LlmPurpose, LlmRequest, LlmResponse, OpenRouterProvider, OpenRouterProviderConfig, Recording, + RecordingProvider, build_inferred_calls_prompt, build_leaf_summary_prompt, }; use clarion_mcp::{ ServerState, @@ -14,6 +17,7 @@ use clarion_mcp::{ filigree::{ EntityAssociation, EntityAssociationsResponse, FiligreeClientError, FiligreeLookup, }, + list_tools, }; use clarion_storage::{ ReaderPool, SummaryCacheEntry, SummaryCacheKey, Writer, pragma, schema, upsert_summary_cache, @@ -34,6 +38,14 @@ fn open_project() -> (tempfile::TempDir, std::path::PathBuf) { (project, db_path) } +fn add_dynamic_source(project_root: &std::path::Path) { + std::fs::write( + project_root.join("demo.py"), + "def entry():\n return mid()\n\ndef mid():\n return target()\n\ndef target():\n return 1\n\ndef dynamic():\n return target()\n", + ) + .expect("write dynamic source"); +} + fn seed_graph(conn: &Connection, project_root: &std::path::Path) { let source_path = project_root.join("demo.py"); std::fs::write( @@ -156,6 +168,7 @@ fn insert_entity( range: Option<(i64, i64)>, parent_id: Option<&str>, ) { + let content_hash = fixture_content_hash(kind, source_path, range); conn.execute( "INSERT INTO entities ( id, plugin_id, kind, name, short_name, parent_id, source_file_path, @@ -172,12 +185,33 @@ fn insert_entity( source_path.display().to_string(), range.map(|(start, _)| start), range.map(|(_, end)| end), - format!("hash-{id}"), + content_hash, ], ) .expect("insert entity"); } +fn fixture_content_hash( + kind: &str, + source_path: &std::path::Path, + range: Option<(i64, i64)>, +) -> String { + if kind == "module" { + return blake3::hash(&std::fs::read(source_path).expect("read module source")) + .to_hex() + .to_string(); + } + let source = std::fs::read_to_string(source_path).expect("read entity source"); + let (start_line, end_line) = range.expect("non-module fixture has source range"); + let start = usize::try_from(start_line - 1).expect("start line fits usize"); + let mut end = usize::try_from(end_line).expect("end line fits usize"); + let lines = source.lines().collect::>(); + end = end.min(lines.len()); + assert!(start < end, "fixture range must overlap source"); + let normalized = lines[start..end].join("\n"); + blake3::hash(normalized.as_bytes()).to_hex().to_string() +} + fn insert_edge( conn: &Connection, kind: &str, @@ -205,16 +239,69 @@ fn insert_edge( } fn insert_unresolved_call_site(conn: &Connection, caller_id: &str, site_key: &str, expr: &str) { + let caller_content_hash: String = conn + .query_row( + "SELECT content_hash FROM entities WHERE id = ?1", + params![caller_id], + |row| row.get(0), + ) + .expect("caller content hash"); conn.execute( "INSERT INTO entity_unresolved_call_sites ( caller_entity_id, caller_content_hash, site_key, site_ordinal, source_file_id, source_byte_start, source_byte_end, callee_expr, created_at ) VALUES (?1, ?2, ?3, 0, 'python:module:demo', 30, 37, ?4, '2026-05-17T00:00:00.000Z')", - params![caller_id, format!("hash-{caller_id}"), site_key, expr], + params![caller_id, caller_content_hash, site_key, expr], ) .expect("insert unresolved call site"); } +fn seed_subsystem(conn: &Connection, project_root: &std::path::Path) -> String { + let extra_source_path = project_root.join("pkg_auth.py"); + std::fs::write(&extra_source_path, "def login():\n return True\n") + .expect("write extra module source"); + insert_entity( + conn, + "python:module:pkg.auth", + "module", + &extra_source_path, + Some((1, 2)), + None, + ); + + let subsystem_id = "core:subsystem:abc123def456".to_owned(); + conn.execute( + "INSERT INTO entities ( + id, plugin_id, kind, name, short_name, properties, created_at, updated_at + ) VALUES ( + ?1, 'core', 'subsystem', 'Subsystem abc123def456', 'abc123def456', + ?2, '2026-05-17T00:00:00.000Z', '2026-05-17T00:00:00.000Z' + )", + params![ + subsystem_id, + json!({"member_count": 2, "modularity_score": 0.42}).to_string(), + ], + ) + .expect("insert subsystem entity"); + insert_edge( + conn, + "in_subsystem", + "python:module:demo", + &subsystem_id, + "resolved", + None, + ); + insert_edge( + conn, + "in_subsystem", + "python:module:pkg.auth", + &subsystem_id, + "resolved", + None, + ); + subsystem_id +} + fn state_for(project_root: &std::path::Path, db_path: &std::path::Path) -> ServerState { let pool = ReaderPool::open(db_path, 2).expect("reader pool"); ServerState::new(project_root.to_path_buf(), pool) @@ -289,9 +376,11 @@ fn expected_inferred_request( target_id: &str, ) -> LlmRequest { let source_excerpt = expected_source_excerpt(project_root, caller_id); + let caller_content_hash = expected_content_hash(project_root, caller_id); + let target_content_hash = expected_content_hash(project_root, target_id); let unresolved_call_sites_json = serde_json::to_string(&vec![json!({ "caller_entity_id": caller_id, - "caller_content_hash": format!("hash-{caller_id}"), + "caller_content_hash": caller_content_hash, "site_key": site_key, "site_ordinal": 0, "source_file_id": "python:module:demo", @@ -309,7 +398,7 @@ fn expected_inferred_request( "source_file_path": source_file_path, "source_line_start": 9, "source_line_end": 10, - "content_hash": format!("hash-{target_id}") + "content_hash": target_content_hash })]) .unwrap(); let prompt = build_inferred_calls_prompt(&InferredCallsPromptInput { @@ -317,13 +406,14 @@ fn expected_inferred_request( caller_source_excerpt: source_excerpt, unresolved_call_sites_json, candidate_entities_json, + max_edges: 8, }); LlmRequest { purpose: LlmPurpose::InferredEdges, model_id: "anthropic/claude-sonnet-4.6".to_owned(), prompt_id: INFERRED_CALLS_PROMPT_VERSION.to_owned(), prompt: prompt.body, - max_output_tokens: 512, + max_output_tokens: 2048, } } @@ -341,6 +431,19 @@ fn expected_source_excerpt(project_root: &std::path::Path, entity_id: &str) -> S lines[start..end.min(lines.len())].concat() } +fn expected_content_hash(project_root: &std::path::Path, entity_id: &str) -> String { + let kind = if entity_id == "python:module:demo" { + "module" + } else { + "function" + }; + fixture_content_hash( + kind, + &project_root.join("demo.py"), + expected_line_range(entity_id), + ) +} + fn expected_line_range(entity_id: &str) -> Option<(i64, i64)> { match entity_id { "python:module:demo" => Some((1, 8)), @@ -415,18 +518,33 @@ impl AnyInferredProvider { #[derive(Debug)] struct AnySummaryProvider { invocations: Mutex>, + output_json: String, delay_ms: u64, estimate_tokens: u64, total_tokens: u32, + cost_usd: f64, } impl AnySummaryProvider { fn new_slow(delay_ms: u64, estimate_tokens: u64, total_tokens: u32) -> Self { Self { invocations: Mutex::new(Vec::new()), + output_json: r#"{"purpose":"concurrent"}"#.to_owned(), delay_ms, estimate_tokens, total_tokens, + cost_usd: 0.0, + } + } + + fn new_output(output_json: &str, total_tokens: u32, cost_usd: f64) -> Self { + Self { + invocations: Mutex::new(Vec::new()), + output_json: output_json.to_owned(), + delay_ms: 0, + estimate_tokens: 0, + total_tokens, + cost_usd, } } @@ -453,11 +571,11 @@ impl LlmProvider for AnySummaryProvider { } Ok(LlmResponse { model_id: request.model_id, - output_json: r#"{"purpose":"concurrent"}"#.to_owned(), + output_json: self.output_json.clone(), input_tokens: 100, output_tokens: 20, total_tokens: self.total_tokens, - cost_usd: 0.0, + cost_usd: self.cost_usd, }) } @@ -581,6 +699,125 @@ async fn call_tool(state: &ServerState, name: &str, arguments: Value) -> Value { serde_json::from_str(text).expect("tool envelope JSON") } +#[test] +fn tools_list_includes_subsystem_members() { + let tools = list_tools(); + let tool = tools + .iter() + .find(|tool| tool.name == "subsystem_members") + .expect("subsystem_members tool definition"); + + assert_eq!( + tool.description, + "List module entities assigned to a subsystem entity." + ); + assert_eq!( + tool.input_schema, + json!({ + "type": "object", + "properties": { + "id": {"type": "string", "minLength": 1} + }, + "required": ["id"], + "additionalProperties": false + }) + ); +} + +#[tokio::test] +async fn subsystem_members_returns_member_modules() { + let (project, db_path) = open_project(); + let conn = Connection::open(&db_path).expect("open sqlite"); + let subsystem_id = seed_subsystem(&conn, project.path()); + drop(conn); + let state = state_for(project.path(), &db_path); + + let envelope = call_tool(&state, "subsystem_members", json!({"id": subsystem_id})).await; + + assert_eq!(envelope["ok"], true); + assert_eq!( + envelope["result"]["subsystem"]["id"], + "core:subsystem:abc123def456" + ); + assert_eq!( + envelope["result"]["subsystem"]["name"], + "Subsystem abc123def456" + ); + assert_eq!( + envelope["result"]["subsystem"]["short_name"], + "abc123def456" + ); + assert_eq!( + envelope["result"]["subsystem"]["properties"]["member_count"], + 2 + ); + assert_eq!( + envelope["result"]["subsystem"]["properties"]["modularity_score"], + 0.42 + ); + let members = envelope["result"]["members"].as_array().unwrap(); + assert_eq!(members.len(), 2); + assert_eq!(members[0]["id"], "python:module:demo"); + assert_eq!(members[1]["id"], "python:module:pkg.auth"); + assert!( + members[0]["source_file_path"] + .as_str() + .unwrap() + .ends_with("demo.py") + ); +} + +#[tokio::test] +async fn subsystem_members_rejects_non_subsystem_id() { + let (project, db_path) = open_project(); + let state = state_for(project.path(), &db_path); + + let envelope = call_tool( + &state, + "subsystem_members", + json!({"id": "python:module:demo"}), + ) + .await; + + assert_eq!(envelope["ok"], false); + assert_eq!(envelope["error"]["code"], "not-a-subsystem"); + assert_eq!(envelope["result"], Value::Null); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn summary_on_subsystem_returns_policy_envelope_without_llm_call() { + let (project, db_path) = open_project(); + let conn = Connection::open(&db_path).expect("open sqlite"); + let subsystem_id = seed_subsystem(&conn, project.path()); + drop(conn); + + let (writer, handle) = Writer::spawn(db_path.clone(), 50, 256).unwrap(); + let provider = Arc::new(AnySummaryProvider::new_output( + r#"{"purpose":"should not run"}"#, + 120, + 0.012, + )); + let state = state_for_summary( + project.path(), + &db_path, + &writer, + provider.clone(), + llm_config(), + ); + + let envelope = call_tool(&state, "summary", json!({"id": subsystem_id})).await; + + assert_eq!(envelope["ok"], true); + assert_eq!(envelope["result"]["available"], false); + assert_eq!(envelope["result"]["reason"], "summary-scope-deferred"); + assert_eq!(envelope["stats_delta"], json!({})); + assert!(provider.invocations().is_empty()); + + drop(state); + drop(writer); + handle.await.unwrap().unwrap(); +} + #[tokio::test] async fn issues_for_returns_unavailable_when_filigree_disabled() { let (project, db_path) = open_project(); @@ -608,7 +845,7 @@ async fn issues_for_includes_contained_entities_and_flags_drift() { vec![association( "filigree-fresh", "python:function:demo.entry", - "hash-python:function:demo.entry", + &expected_content_hash(project.path(), "python:function:demo.entry"), )], ) .with_response( @@ -656,7 +893,7 @@ async fn issues_for_respects_include_contained_false() { vec![association( "filigree-module", "python:module:demo", - "hash-python:module:demo", + &expected_content_hash(project.path(), "python:module:demo"), )], ) .with_response( @@ -664,7 +901,7 @@ async fn issues_for_respects_include_contained_false() { vec![association( "filigree-entry", "python:function:demo.entry", - "hash-python:function:demo.entry", + &expected_content_hash(project.path(), "python:function:demo.entry"), )], ), ); @@ -693,7 +930,7 @@ async fn issues_for_truncates_at_issue_cap() { association( &format!("filigree-{idx:03}"), "python:function:demo.entry", - "hash-python:function:demo.entry", + &expected_content_hash(project.path(), "python:function:demo.entry"), ) }) .collect(); @@ -723,7 +960,7 @@ async fn issues_for_stops_filigree_calls_after_issue_cap() { association( &format!("filigree-{idx:03}"), "python:module:demo", - "hash-python:module:demo", + &expected_content_hash(project.path(), "python:module:demo"), ) }) .collect(); @@ -735,7 +972,7 @@ async fn issues_for_stops_filigree_calls_after_issue_cap() { vec![association( "filigree-entry", "python:function:demo.entry", - "hash-python:function:demo.entry", + &expected_content_hash(project.path(), "python:function:demo.entry"), )], ), ); @@ -812,6 +1049,111 @@ async fn summary_cold_miss_records_provider_response_then_hits_cache() { handle.await.unwrap().unwrap(); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn summary_invalid_json_preserves_usage_accounting() { + let (project, db_path) = open_project(); + let (writer, handle) = Writer::spawn(db_path.clone(), 50, 256).unwrap(); + let provider = Arc::new(AnySummaryProvider::new_output("not-json", 120, 0.012)); + let state = state_for_summary( + project.path(), + &db_path, + &writer, + provider.clone(), + llm_config(), + ); + + let envelope = call_tool( + &state, + "summary", + json!({"id": "python:function:demo.entry"}), + ) + .await; + + assert_eq!(envelope["ok"], false); + assert_eq!(envelope["error"]["code"], "llm-invalid-json"); + assert_eq!(envelope["stats_delta"]["summary_cache_misses_total"], 1); + assert_eq!(envelope["stats_delta"]["summary_tokens_input"], 100); + assert_eq!(envelope["stats_delta"]["summary_tokens_output"], 20); + assert_eq!(envelope["stats_delta"]["summary_tokens_total"], 120); + assert_eq!(envelope["stats_delta"]["summary_cost_usd"], 0.012); + assert_eq!(envelope["stats_delta"]["llm_invalid_json_total"], 1); + assert_eq!(provider.invocations().len(), 1); + + drop(state); + drop(writer); + handle.await.unwrap().unwrap(); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn summary_openrouter_provider_runs_outside_async_runtime() { + use std::io::{Read, Write}; + use std::net::TcpListener; + + let (project, db_path) = open_project(); + let listener = TcpListener::bind("127.0.0.1:0").expect("bind test OpenRouter"); + let addr = listener.local_addr().expect("test OpenRouter addr"); + let http = std::thread::spawn(move || { + let (mut stream, _) = listener.accept().expect("accept OpenRouter request"); + let mut request = [0_u8; 8192]; + let read = stream.read(&mut request).expect("read OpenRouter request"); + let request = String::from_utf8_lossy(&request[..read]); + assert!(request.contains(r#""response_format":{"json_schema":{"name":"clarion_summary""#)); + let body = r#"{ + "id": "gen-01", + "object": "chat.completion", + "created": 1779000000, + "model": "anthropic/claude-sonnet-4.6", + "choices": [ + { + "finish_reason": "stop", + "native_finish_reason": "stop", + "message": { + "role": "assistant", + "content": "{\"purpose\":\"demo\",\"behavior\":\"returns mid\",\"relationships\":\"calls mid\",\"risks\":\"\"}" + } + } + ], + "usage": {"prompt_tokens": 100, "completion_tokens": 20, "total_tokens": 120} + }"#; + write!( + stream, + "HTTP/1.1 200 OK\r\ncontent-type: application/json\r\ncontent-length: {}\r\n\r\n{}", + body.len(), + body + ) + .expect("write OpenRouter response"); + }); + let provider = Arc::new( + OpenRouterProvider::from_config(OpenRouterProviderConfig { + api_key: Some("secret".to_owned()), + allow_live_provider: true, + model_id: "anthropic/claude-sonnet-4.6".to_owned(), + endpoint_url: format!("http://{addr}/api/v1"), + referer: "https://github.com/qacona/clarion".to_owned(), + title: "Clarion Test".to_owned(), + }) + .expect("OpenRouter provider"), + ); + let (writer, handle) = Writer::spawn(db_path.clone(), 50, 256).unwrap(); + let state = state_for_summary(project.path(), &db_path, &writer, provider, llm_config()); + + let envelope = call_tool( + &state, + "summary", + json!({"id": "python:function:demo.entry"}), + ) + .await; + + assert_eq!(envelope["ok"], true); + assert_eq!(envelope["result"]["summary"]["purpose"], "demo"); + assert_eq!(envelope["stats_delta"]["summary_tokens_total"], 120); + + drop(state); + drop(writer); + handle.await.unwrap().unwrap(); + http.join().expect("OpenRouter server thread"); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn summary_prompt_uses_entity_source_range_not_whole_file() { let (project, db_path) = open_project(); @@ -851,6 +1193,55 @@ async fn summary_prompt_uses_entity_source_range_not_whole_file() { handle.await.unwrap().unwrap(); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn summary_cold_miss_refuses_live_source_drift() { + let (project, db_path) = open_project(); + let original_hash = blake3::hash("def entry():\n return mid()".as_bytes()) + .to_hex() + .to_string(); + let conn = Connection::open(&db_path).unwrap(); + conn.execute( + "UPDATE entities SET content_hash = ?1 WHERE id = 'python:function:demo.entry'", + params![original_hash], + ) + .unwrap(); + drop(conn); + fs::write( + project.path().join("demo.py"), + "def entry():\n return changed()\n\ndef mid():\n return target()\n\ndef target():\n return 1\n", + ) + .unwrap(); + + let (writer, handle) = Writer::spawn(db_path.clone(), 50, 256).unwrap(); + let provider = Arc::new(AnySummaryProvider::new_output( + r#"{"purpose":"should not run"}"#, + 120, + 0.0, + )); + let state = state_for_summary( + project.path(), + &db_path, + &writer, + provider.clone(), + llm_config(), + ); + + let envelope = call_tool( + &state, + "summary", + json!({"id": "python:function:demo.entry"}), + ) + .await; + + assert_eq!(envelope["ok"], false); + assert_eq!(envelope["error"]["code"], "content-drift"); + assert_eq!(provider.invocations().len(), 0); + + drop(state); + drop(writer); + handle.await.unwrap().unwrap(); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn summary_cache_hit_reports_stale_semantic_when_graph_counts_drift() { let (project, db_path) = open_project(); @@ -860,7 +1251,7 @@ async fn summary_cache_hit_reports_stale_semantic_when_graph_counts_drift() { &SummaryCacheEntry { key: SummaryCacheKey { entity_id: "python:function:demo.entry".to_owned(), - content_hash: "hash-python:function:demo.entry".to_owned(), + content_hash: expected_content_hash(project.path(), "python:function:demo.entry"), prompt_template_id: LEAF_SUMMARY_PROMPT_TEMPLATE_ID.to_owned(), model_tier: "anthropic/claude-sonnet-4.6".to_owned(), guidance_fingerprint: "guidance-empty".to_owned(), @@ -908,7 +1299,7 @@ async fn summary_expired_cache_row_is_refreshed_by_recording_provider() { &SummaryCacheEntry { key: SummaryCacheKey { entity_id: "python:function:demo.entry".to_owned(), - content_hash: "hash-python:function:demo.entry".to_owned(), + content_hash: expected_content_hash(project.path(), "python:function:demo.entry"), prompt_template_id: LEAF_SUMMARY_PROMPT_TEMPLATE_ID.to_owned(), model_tier: "anthropic/claude-sonnet-4.6".to_owned(), guidance_fingerprint: "guidance-empty".to_owned(), @@ -1192,6 +1583,7 @@ async fn callers_of_defaults_to_resolved_and_expands_ambiguous_candidates() { async fn callers_of_inferred_dispatches_and_materializes_recording_result() { let (project, db_path) = open_project(); let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); let source_path = project.path().join("demo.py"); insert_entity( &conn, @@ -1263,6 +1655,7 @@ async fn callers_of_inferred_dispatches_and_materializes_recording_result() { async fn inferred_dispatch_prompt_uses_caller_source_range_not_whole_file() { let (project, db_path) = open_project(); let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); let source_path = project.path().join("demo.py"); insert_entity( &conn, @@ -1321,6 +1714,7 @@ async fn inferred_dispatch_prompt_uses_caller_source_range_not_whole_file() { async fn callers_of_inferred_coalesces_concurrent_cold_requests() { let (project, db_path) = open_project(); let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); let source_path = project.path().join("demo.py"); insert_entity( &conn, @@ -1373,6 +1767,138 @@ async fn callers_of_inferred_coalesces_concurrent_cold_requests() { handle.await.unwrap().unwrap(); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn callers_of_inferred_invalid_json_preserves_usage_accounting() { + let (project, db_path) = open_project(); + let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); + let source_path = project.path().join("demo.py"); + insert_entity( + &conn, + "python:function:demo.dynamic", + "function", + &source_path, + Some((9, 10)), + Some("python:module:demo"), + ); + insert_unresolved_call_site( + &conn, + "python:function:demo.entry", + "site-dynamic", + "dynamic", + ); + drop(conn); + + let (writer, handle) = Writer::spawn(db_path.clone(), 50, 256).unwrap(); + let provider = Arc::new(AnyInferredProvider::new("not-json")); + let state = state_for_summary( + project.path(), + &db_path, + &writer, + provider.clone(), + llm_config(), + ); + + let envelope = call_tool( + &state, + "callers_of", + json!({"id": "python:function:demo.dynamic", "confidence": "inferred"}), + ) + .await; + + assert_eq!(envelope["ok"], false); + assert_eq!(envelope["error"]["code"], "llm-invalid-json"); + assert_eq!(envelope["stats_delta"]["inferred_dispatch_misses_total"], 1); + assert_eq!(envelope["stats_delta"]["inferred_tokens_input"], 100); + assert_eq!(envelope["stats_delta"]["inferred_tokens_output"], 20); + assert_eq!(envelope["stats_delta"]["inferred_tokens_total"], 120); + assert_eq!(envelope["stats_delta"]["inferred_cost_usd"], 0.0); + assert_eq!(envelope["stats_delta"]["llm_invalid_json_total"], 1); + assert_eq!(provider.invocations().len(), 1); + + drop(state); + drop(writer); + handle.await.unwrap().unwrap(); +} + +// clarion-df58379de4: when the LLM hallucinates a `target_id` that isn't in the +// `entities` table, the inferred-dispatch path must drop that edge before +// reaching the writer-actor's FK-protected INSERT. The cache row must still be +// persisted so a warm rerun does not re-burn LLM tokens, and the dispatch must +// return `ok=true` with a `inferred_unresolved_targets_dropped_total` count. +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn callers_of_inferred_drops_targets_missing_from_entities_table() { + let (project, db_path) = open_project(); + let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); + let source_path = project.path().join("demo.py"); + insert_entity( + &conn, + "python:function:demo.dynamic", + "function", + &source_path, + Some((9, 10)), + Some("python:module:demo"), + ); + insert_unresolved_call_site( + &conn, + "python:function:demo.entry", + "site-dynamic", + "dynamic", + ); + drop(conn); + + let (writer, handle) = Writer::spawn(db_path.clone(), 50, 256).unwrap(); + let provider = Arc::new(AnyInferredProvider::new( + r#"{"edges":[{"site_key":"site-dynamic","target_id":"python:function:nonexistent.hallucinated","confidence":0.91,"rationale":"name match"}]}"#, + )); + let state = state_for_summary( + project.path(), + &db_path, + &writer, + provider.clone(), + llm_config(), + ); + + let envelope = call_tool( + &state, + "callers_of", + json!({"id": "python:function:demo.dynamic", "confidence": "inferred"}), + ) + .await; + + assert_eq!(envelope["ok"], true, "envelope was {envelope}"); + assert_eq!( + envelope["stats_delta"]["inferred_unresolved_targets_dropped_total"], + 1 + ); + assert_eq!( + envelope["stats_delta"]["inferred_edges_materialized_total"], + 0 + ); + assert_eq!(envelope["result"]["callers"].as_array().unwrap().len(), 0); + assert_eq!(provider.invocations().len(), 1); + + // Warm rerun: cache row must have been persisted even though the LLM + // proposed an unresolvable target, so we do not re-dispatch. + let warm = call_tool( + &state, + "callers_of", + json!({"id": "python:function:demo.dynamic", "confidence": "inferred"}), + ) + .await; + assert_eq!(warm["ok"], true); + assert_eq!(provider.invocations().len(), 1, "cache miss on warm rerun"); + assert_eq!( + warm["stats_delta"]["inferred_unresolved_targets_dropped_total"], + 1 + ); + + drop(state); + drop(writer); + handle.await.unwrap().unwrap(); +} + #[tokio::test] async fn execution_paths_from_reports_edge_cap_truncation() { let (project, db_path) = open_project(); @@ -1395,6 +1921,7 @@ async fn execution_paths_from_reports_edge_cap_truncation() { async fn execution_paths_from_inferred_dispatches_start_caller() { let (project, db_path) = open_project(); let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); let source_path = project.path().join("demo.py"); insert_entity( &conn, @@ -1455,6 +1982,7 @@ async fn execution_paths_from_inferred_dispatches_start_caller() { async fn execution_paths_from_inferred_dispatches_reached_callers() { let (project, db_path) = open_project(); let conn = Connection::open(&db_path).unwrap(); + add_dynamic_source(project.path()); let source_path = project.path().join("demo.py"); insert_entity( &conn, diff --git a/crates/clarion-plugin-fixture/Cargo.toml b/crates/clarion-plugin-fixture/Cargo.toml index 21dfca74..3c46f905 100644 --- a/crates/clarion-plugin-fixture/Cargo.toml +++ b/crates/clarion-plugin-fixture/Cargo.toml @@ -16,3 +16,6 @@ path = "src/main.rs" [dependencies] clarion-core = { path = "../clarion-core", version = "0.1.0-dev" } serde_json.workspace = true + +[target.'cfg(unix)'.dependencies] +nix = { workspace = true, features = ["mman", "signal"] } diff --git a/crates/clarion-plugin-fixture/src/main.rs b/crates/clarion-plugin-fixture/src/main.rs index bd4a6922..b1b4453a 100644 --- a/crates/clarion-plugin-fixture/src/main.rs +++ b/crates/clarion-plugin-fixture/src/main.rs @@ -75,6 +75,13 @@ fn main() { send_result(&mut writer, id, serde_json::to_value(result).unwrap()); } "analyze_file" => { + if std::env::var_os("CLARION_FIXTURE_EXCEED_RLIMIT_AS").is_some() { + #[cfg(unix)] + exceed_rlimit_as(); + #[cfg(not(unix))] + std::process::exit(1); + } + // Extract the file_path from params. let file_path = raw .get("params") @@ -126,3 +133,52 @@ fn send_result(writer: &mut impl Write, id: i64, result: Value) { write_frame(writer, &frame).expect("write frame"); writer.flush().expect("flush"); } + +#[cfg(unix)] +fn exceed_rlimit_as() -> ! { + use std::num::NonZeroUsize; + + const FIRST_REQUEST_BYTES: usize = 128 * 1024 * 1024; + let mut mappings = Vec::new(); + mappings + .try_reserve_exact(1024) + .expect("reserve mapping handles before memory pressure"); + let mut request_bytes = FIRST_REQUEST_BYTES; + loop { + let length = NonZeroUsize::new(request_bytes).expect("non-zero request"); + // SAFETY: This fixture intentionally asks the kernel for anonymous + // address space after the host has applied RLIMIT_AS. The mapping is + // never dereferenced; it is only held so successful probes continue to + // count against the child process until the next probe fails. + let mapped = { + #[allow(unsafe_code)] + unsafe { + nix::sys::mman::mmap_anonymous( + None, + length, + nix::sys::mman::ProtFlags::PROT_NONE, + nix::sys::mman::MapFlags::MAP_PRIVATE, + ) + } + }; + match mapped { + Ok(ptr) => { + mappings.push(ptr); + let next_request = request_bytes.saturating_mul(2); + if next_request == request_bytes { + terminate_after_rlimit_failure(); + } + request_bytes = next_request; + } + Err(_) => { + terminate_after_rlimit_failure(); + } + } + } +} + +#[cfg(unix)] +fn terminate_after_rlimit_failure() -> ! { + let _ = nix::sys::signal::kill(nix::unistd::Pid::this(), nix::sys::signal::Signal::SIGKILL); + std::process::abort(); +} diff --git a/crates/clarion-storage/migrations/0001_initial_schema.sql b/crates/clarion-storage/migrations/0001_initial_schema.sql index a0cb4bad..19727874 100644 --- a/crates/clarion-storage/migrations/0001_initial_schema.sql +++ b/crates/clarion-storage/migrations/0001_initial_schema.sql @@ -11,8 +11,9 @@ -- as long as no external operator has produced a `.clarion/clarion.db` from -- a published Clarion build. The retirement trigger names exactly that -- condition; once it fires, all schema changes stack as 0002_*.sql etc. --- The 2026-05-03 edits (guidance vocabulary rename per ADR-024) were --- applied under this policy. +-- The 2026-05-03 edits (guidance vocabulary rename per ADR-024) and the +-- 2026-05-18 edits (CHECK constraints on closed-vocabulary TEXT columns per +-- ADR-031) were both applied under this policy. -- ============================================================================ BEGIN; @@ -29,6 +30,9 @@ CREATE TABLE schema_migrations ( CREATE TABLE entities ( id TEXT PRIMARY KEY, plugin_id TEXT NOT NULL, + -- ADR-031: plugin-extensible vocabulary (ADR-022 reserves entity-kind + -- declaration to the plugin manifest); no CHECK by policy. Writer-actor + -- + manifest acceptance is the enforcement layer. kind TEXT NOT NULL, name TEXT NOT NULL, short_name TEXT NOT NULL, @@ -59,17 +63,25 @@ CREATE INDEX ix_entities_content_hash ON entities(content_hash); -- Tags (denormalised) CREATE TABLE entity_tags ( entity_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, + plugin_id TEXT NOT NULL, tag TEXT NOT NULL, - PRIMARY KEY (entity_id, tag) + PRIMARY KEY (entity_id, plugin_id, tag) ); CREATE INDEX ix_entity_tags_tag ON entity_tags(tag); +CREATE INDEX ix_entity_tags_plugin_tag ON entity_tags(plugin_id, tag); -- Edges. Natural PK (kind, from_id, to_id) per ADR-026 decision 4 (B.3). -- Synthetic `id` column dropped: no Sprint-1 or B.3 query selects edges by -- `id`; the natural composite is stable across re-analyze, and the only -- finding-attachment cross-reference (findings.entity_id) points at entities, --- not edges. WITHOUT ROWID drops the now-redundant rowid pages. +-- not edges. The properties bag is evidence/metadata, not identity; callers +-- that need multiple observations for the same relationship merge them into +-- one edge row. WITHOUT ROWID drops the now-redundant rowid pages. CREATE TABLE edges ( + -- ADR-031: plugin-extensible vocabulary (ADR-022 admits plugin-declared + -- edge kinds beyond the four core-reserved structural ones); no CHECK by + -- policy. Writer-actor `enforce_edge_contract` is the enforcement layer + -- for the v0.1 9-value ontology. kind TEXT NOT NULL, from_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, to_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, @@ -77,6 +89,7 @@ CREATE TABLE edges ( source_file_id TEXT REFERENCES entities(id), source_byte_start INTEGER, source_byte_end INTEGER, + -- ADR-031 precedent: closed core-owned vocabulary; values per ADR-028. confidence TEXT NOT NULL DEFAULT 'resolved' CHECK (confidence IN ('resolved', 'ambiguous', 'inferred')), PRIMARY KEY (kind, from_id, to_id) @@ -91,10 +104,16 @@ CREATE TABLE findings ( id TEXT PRIMARY KEY, tool TEXT NOT NULL, tool_version TEXT NOT NULL, - run_id TEXT NOT NULL, + run_id TEXT NOT NULL REFERENCES runs(id) ON DELETE CASCADE, rule_id TEXT NOT NULL, - kind TEXT NOT NULL, - severity TEXT NOT NULL, + -- ADR-031: closed core-owned vocabulary; values per ADR-004 + + -- detailed-design.md §3. + kind TEXT NOT NULL + CHECK (kind IN ('defect', 'fact', 'classification', 'metric', 'suggestion')), + -- ADR-031: closed core-owned vocabulary; values per ADR-017 (Clarion + -- internal severity, pre-mapping to Filigree wire). + severity TEXT NOT NULL + CHECK (severity IN ('INFO', 'WARN', 'ERROR', 'CRITICAL', 'NONE')), confidence REAL, confidence_basis TEXT, entity_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, @@ -104,7 +123,10 @@ CREATE TABLE findings ( properties TEXT NOT NULL, supports TEXT NOT NULL, supported_by TEXT NOT NULL, - status TEXT NOT NULL, + -- ADR-031: closed core-owned vocabulary; values per + -- detailed-design.md §3 finding lifecycle. + status TEXT NOT NULL + CHECK (status IN ('open', 'acknowledged', 'suppressed', 'promoted_to_issue')), suppression_reason TEXT, filigree_issue_id TEXT, created_at TEXT NOT NULL, @@ -131,6 +153,7 @@ CREATE TABLE summary_cache ( last_accessed_at TEXT NOT NULL, caller_count INTEGER NOT NULL, fan_out INTEGER NOT NULL, + -- ADR-031 precedent: closed core-owned vocabulary; boolean-shaped INTEGER. stale_semantic INTEGER NOT NULL DEFAULT 0 CHECK (stale_semantic IN (0, 1)), PRIMARY KEY (entity_id, content_hash, prompt_template_id, model_tier, guidance_fingerprint) ); @@ -175,7 +198,11 @@ CREATE TABLE runs ( completed_at TEXT, config TEXT NOT NULL, stats TEXT NOT NULL, + -- ADR-031: closed core-owned vocabulary; terminal values from the + -- `RunStatus` enum (commands.rs); 'running' is the in-flight literal + -- inserted by BeginRun (writer.rs). status TEXT NOT NULL + CHECK (status IN ('running', 'skipped_no_plugins', 'completed', 'failed')) ); -- FTS5 for text search diff --git a/crates/clarion-storage/src/commands.rs b/crates/clarion-storage/src/commands.rs index 7c7b4990..7e609f16 100644 --- a/crates/clarion-storage/src/commands.rs +++ b/crates/clarion-storage/src/commands.rs @@ -106,6 +106,32 @@ pub struct InferredEdgeWriteStats { pub skipped_static_duplicates: u64, } +/// Plain-old-data finding record as seen by the writer. JSON-typed fields are +/// serialized by the caller and inserted verbatim; lifecycle status is owned by +/// the writer and starts as `open`. +#[derive(Debug, Clone)] +pub struct FindingRecord { + pub id: String, + pub tool: String, + pub tool_version: String, + pub run_id: String, + pub rule_id: String, + pub kind: String, + pub severity: String, + pub confidence: Option, + pub confidence_basis: Option, + pub entity_id: String, + pub related_entities_json: String, + pub message: String, + pub evidence_json: String, + pub properties_json: String, + pub supports_json: String, + pub supported_by_json: String, + /// ISO-8601 UTC; writer inserts verbatim. + pub created_at: String, + pub updated_at: String, +} + /// All writer operations as a single enum so the actor loop exhausts /// everything via one match. #[derive(Debug)] @@ -131,6 +157,15 @@ pub enum WriterCmd { /// `Writer::dropped_edges_total` on dedupe. Also advances the per-batch /// write counter — edges and entities share one batch boundary. InsertEdge { edge: Box, ack: Ack<()> }, + /// Insert one finding. The writer initializes lifecycle status to `open` + /// and leaves suppression / Filigree-link fields empty. + InsertFinding { + finding: Box, + ack: Ack<()>, + }, + /// Commit the current analyze batch and reopen it so readers on separate + /// `SQLite` connections can observe graph rows before `CommitRun`. + FlushRunBatch { ack: Ack<()> }, /// Upsert one inferred-edge cache row and materialize its current inferred /// call edges. This query-time MCP write does not require an active /// analyze run and does not use scan-time edge contracts. diff --git a/crates/clarion-storage/src/error.rs b/crates/clarion-storage/src/error.rs index e159fab3..d9a775dc 100644 --- a/crates/clarion-storage/src/error.rs +++ b/crates/clarion-storage/src/error.rs @@ -46,3 +46,70 @@ pub enum StorageError { } pub type Result = std::result::Result; + +impl StorageError { + /// `true` iff the underlying rusqlite error is a foreign-key + /// constraint violation (`SQLite` extended code 787). The MCP envelope + /// layer uses this to mark such failures `retryable=false`, because + /// a deterministic FK violation against the same row will recur on + /// retry and re-burn LLM tokens (clarion-df58379de4). + #[must_use] + pub fn is_foreign_key_violation(&self) -> bool { + match self { + Self::Sqlite(rusqlite::Error::SqliteFailure(err, _)) => { + err.extended_code == rusqlite::ffi::SQLITE_CONSTRAINT_FOREIGNKEY + } + _ => false, + } + } +} + +#[cfg(test)] +mod tests { + use super::*; + use rusqlite::Connection; + + #[test] + fn is_foreign_key_violation_detects_sqlite_fk_breach() { + let conn = Connection::open_in_memory().unwrap(); + conn.execute_batch( + "PRAGMA foreign_keys = ON; \ + CREATE TABLE parent (id TEXT PRIMARY KEY); \ + CREATE TABLE child (id TEXT PRIMARY KEY, parent_id TEXT REFERENCES parent(id));", + ) + .unwrap(); + let raw = conn + .execute( + "INSERT INTO child (id, parent_id) VALUES ('c1', 'absent')", + [], + ) + .expect_err("FK violation should fail the insert"); + let err: StorageError = raw.into(); + assert!( + err.is_foreign_key_violation(), + "expected FK classifier to recognise SQLITE_CONSTRAINT_FOREIGNKEY (787), got {err}" + ); + } + + #[test] + fn is_foreign_key_violation_rejects_other_constraint_breaches() { + let conn = Connection::open_in_memory().unwrap(); + conn.execute("CREATE TABLE t (id TEXT PRIMARY KEY)", []) + .unwrap(); + conn.execute("INSERT INTO t VALUES ('a')", []).unwrap(); + let raw = conn + .execute("INSERT INTO t VALUES ('a')", []) + .expect_err("PK collision should fail the insert"); + let err: StorageError = raw.into(); + assert!( + !err.is_foreign_key_violation(), + "PK collision should not be classified as FK violation: {err}" + ); + } + + #[test] + fn is_foreign_key_violation_returns_false_for_non_sqlite_errors() { + let err = StorageError::WriterGone; + assert!(!err.is_foreign_key_violation()); + } +} diff --git a/crates/clarion-storage/src/lib.rs b/crates/clarion-storage/src/lib.rs index b62ae294..62b62589 100644 --- a/crates/clarion-storage/src/lib.rs +++ b/crates/clarion-storage/src/lib.rs @@ -21,15 +21,21 @@ pub use cache::{ upsert_summary_cache, }; pub use commands::{ - EdgeRecord, EntityRecord, InferredCallEdgeRecord, InferredEdgeWriteStats, RunStatus, WriterCmd, + EdgeRecord, EntityRecord, FindingRecord, InferredCallEdgeRecord, InferredEdgeWriteStats, + RunStatus, WriterCmd, }; pub use error::{Result, StorageError}; pub use query::{ - CallEdgeMatch, ContainedEntities, EntityRow, UnresolvedCallSiteRow, call_edges_from, + CallEdgeMatch, ContainedEntities, EntityRow, ModuleDependencyEdge, ReferenceDirection, + ReferenceEdgeMatch, SubsystemMember, UnresolvedCallSiteRow, call_edges_from, call_edges_targeting, candidate_entities_for_unresolved_sites, child_entity_ids, - contained_entity_ids, entity_at_line, entity_by_id, find_entities, normalize_source_path, - unresolved_call_sites_for_caller, unresolved_callers_for_target, + contained_entity_ids, entity_at_line, entity_by_id, existing_entity_ids, find_entities, + module_dependency_edges, normalize_source_path, reference_edges_for_entity, + subsystem_for_member, subsystem_members, unresolved_call_sites_for_caller, + unresolved_callers_for_target, }; pub use reader::ReaderPool; pub use unresolved::{UnresolvedCallSiteRecord, replace_unresolved_call_sites_for_caller}; -pub use writer::{DEFAULT_BATCH_SIZE, DEFAULT_CHANNEL_CAPACITY, Writer}; +pub use writer::{ + DEFAULT_BATCH_SIZE, DEFAULT_CHANNEL_CAPACITY, Writer, known_scan_time_edge_kinds, +}; diff --git a/crates/clarion-storage/src/query.rs b/crates/clarion-storage/src/query.rs index 80f5a099..28140237 100644 --- a/crates/clarion-storage/src/query.rs +++ b/crates/clarion-storage/src/query.rs @@ -1,10 +1,10 @@ //! Read-side query helpers used by the MCP navigation surface. -use std::collections::BTreeSet; +use std::collections::{BTreeMap, BTreeSet, HashSet}; use std::path::{Component, Path, PathBuf}; use clarion_core::EdgeConfidence; -use rusqlite::{Connection, OptionalExtension, Row, params}; +use rusqlite::{Connection, OptionalExtension, Row, params, params_from_iter}; use crate::{Result, StorageError}; @@ -57,6 +57,38 @@ pub struct UnresolvedCallSiteRow { pub callee_expr: String, } +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct ReferenceEdgeMatch { + pub neighbor_id: String, + pub confidence: EdgeConfidence, + pub source_file_id: Option, + pub source_byte_start: Option, + pub source_byte_end: Option, +} + +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct ModuleDependencyEdge { + pub from_module_id: String, + pub to_module_id: String, + pub reference_count: u64, + pub edge_kinds: Vec, +} + +const MODULE_ANCESTOR_MAX_DEPTH: i64 = 32; + +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct SubsystemMember { + pub id: String, + pub name: String, + pub source_file_path: Option, +} + +#[derive(Debug, Clone, Copy, PartialEq, Eq)] +pub enum ReferenceDirection { + In, + Out, +} + #[derive(Debug, Clone)] struct StoredCallEdge { from_id: String, @@ -68,6 +100,14 @@ struct StoredCallEdge { properties_json: Option, } +struct StoredDependencyEdge { + from_id: String, + to_id: String, + kind: String, + confidence: EdgeConfidence, + properties_json: Option, +} + const ENTITY_COLUMNS: &str = "\ id, plugin_id, kind, name, short_name, parent_id, source_file_id, \ source_file_path, source_byte_start, source_byte_end, source_line_start, \ @@ -110,6 +150,32 @@ pub fn entity_by_id(conn: &Connection, entity_id: &str) -> Result Result> { + if candidates.is_empty() { + return Ok(HashSet::new()); + } + let mut found = HashSet::with_capacity(candidates.len()); + for chunk in candidates.chunks(500) { + let placeholders = std::iter::repeat_n("?", chunk.len()) + .collect::>() + .join(", "); + let sql = format!("SELECT id FROM entities WHERE id IN ({placeholders})"); + let mut stmt = conn.prepare(&sql)?; + let rows = stmt.query_map(params_from_iter(chunk.iter()), |row| { + row.get::<_, String>(0) + })?; + for row in rows { + found.insert(row?); + } + } + Ok(found) +} + pub fn entity_at_line( conn: &Connection, source_file_path: &str, @@ -331,6 +397,180 @@ pub fn unresolved_callers_for_target( .map_err(StorageError::from) } +pub fn reference_edges_for_entity( + conn: &Connection, + entity_id: &str, + direction: ReferenceDirection, +) -> Result> { + let sql = match direction { + ReferenceDirection::In => { + "SELECT from_id, confidence, source_file_id, source_byte_start, source_byte_end \ + FROM edges \ + WHERE kind = 'references' AND to_id = ?1 \ + ORDER BY from_id, source_byte_start, source_byte_end" + } + ReferenceDirection::Out => { + "SELECT to_id, confidence, source_file_id, source_byte_start, source_byte_end \ + FROM edges \ + WHERE kind = 'references' AND from_id = ?1 \ + ORDER BY to_id, source_byte_start, source_byte_end" + } + }; + let mut stmt = conn.prepare(sql)?; + let rows = stmt.query_map(params![entity_id], map_reference_edge_match)?; + rows.collect::, _>>() + .map_err(StorageError::from) +} + +pub fn module_dependency_edges( + conn: &Connection, + edge_types: &[&str], +) -> Result> { + if edge_types.is_empty() { + return Ok(Vec::new()); + } + + // v0.1 assumes a wipe-and-rerun analyze workflow, so clustering reads the + // whole static graph. v0.2 incremental analyze needs run-scoped edge + // provenance before this helper can filter by current run. + let ancestors = module_ancestor_map(conn)?; + let placeholders = std::iter::repeat_n("?", edge_types.len()) + .collect::>() + .join(", "); + let sql = format!( + "SELECT from_id, to_id, kind, confidence, properties \ + FROM edges \ + WHERE kind IN ({placeholders}) \ + AND confidence != 'inferred' \ + ORDER BY from_id, to_id, kind", + ); + let mut stmt = conn.prepare(&sql)?; + let rows = stmt.query_map(params_from_iter(edge_types.iter().copied()), |row| { + let raw_confidence: String = row.get(3)?; + Ok(StoredDependencyEdge { + from_id: row.get(0)?, + to_id: row.get(1)?, + kind: row.get(2)?, + confidence: parse_confidence(&raw_confidence)?, + properties_json: row.get(4)?, + }) + })?; + + let mut grouped: BTreeMap<(String, String), (u64, BTreeSet)> = BTreeMap::new(); + for row in rows { + let edge = row?; + let Some(from_modules) = ancestors.get(&edge.from_id) else { + continue; + }; + for target_id in dependency_edge_target_ids(&edge) { + let Some(to_modules) = ancestors.get(&target_id) else { + continue; + }; + for from_module_id in from_modules { + for to_module_id in to_modules { + if from_module_id == to_module_id { + continue; + } + let (reference_count, edge_kinds) = grouped + .entry((from_module_id.clone(), to_module_id.clone())) + .or_insert_with(|| (0, BTreeSet::new())); + *reference_count += 1; + edge_kinds.insert(edge.kind.clone()); + } + } + } + } + + Ok(grouped + .into_iter() + .map( + |((from_module_id, to_module_id), (reference_count, edge_kinds))| { + ModuleDependencyEdge { + from_module_id, + to_module_id, + reference_count, + edge_kinds: edge_kinds.into_iter().collect(), + } + }, + ) + .collect()) +} + +fn module_ancestor_map(conn: &Connection) -> Result>> { + let mut stmt = conn.prepare( + "WITH RECURSIVE module_ancestors(entity_id, module_id, depth) AS ( \ + SELECT id, id, 0 FROM entities WHERE kind = 'module' \ + UNION ALL \ + SELECT child.to_id, module_ancestors.module_id, module_ancestors.depth + 1 \ + FROM edges child \ + JOIN module_ancestors ON module_ancestors.entity_id = child.from_id \ + WHERE child.kind = 'contains' \ + AND module_ancestors.depth < ?1 \ + ) \ + SELECT DISTINCT entity_id, module_id \ + FROM module_ancestors \ + ORDER BY entity_id, module_id", + )?; + let rows = stmt.query_map(params![MODULE_ANCESTOR_MAX_DEPTH], |row| { + Ok((row.get::<_, String>(0)?, row.get::<_, String>(1)?)) + })?; + let mut ancestors: BTreeMap> = BTreeMap::new(); + for row in rows { + let (entity_id, module_id) = row?; + ancestors.entry(entity_id).or_default().insert(module_id); + } + Ok(ancestors) +} + +fn dependency_edge_target_ids(edge: &StoredDependencyEdge) -> BTreeSet { + let mut targets = BTreeSet::from([edge.to_id.clone()]); + if edge.kind == "calls" && edge.confidence == EdgeConfidence::Ambiguous { + targets.extend(candidate_ids(edge.properties_json.as_deref())); + } + targets +} + +pub fn subsystem_members(conn: &Connection, subsystem_id: &str) -> Result> { + let mut stmt = conn.prepare( + "SELECT entities.id, entities.name, entities.source_file_path \ + FROM edges \ + JOIN entities ON entities.id = edges.from_id \ + WHERE edges.kind = 'in_subsystem' \ + AND edges.to_id = ?1 \ + AND entities.kind = 'module' \ + ORDER BY entities.name, entities.id", + )?; + let rows = stmt.query_map(params![subsystem_id], |row| { + Ok(SubsystemMember { + id: row.get(0)?, + name: row.get(1)?, + source_file_path: row.get(2)?, + }) + })?; + rows.collect::, _>>() + .map_err(StorageError::from) +} + +pub fn subsystem_for_member(conn: &Connection, module_id: &str) -> Result> { + // Reserved for v0.2 neighborhood / issues_for enrichment. v0.1's MCP + // surface exposes subsystem_members, but keeping this inverse lookup here + // preserves the query contract and tests until those callers land. + conn.query_row( + "SELECT edges.to_id \ + FROM edges \ + JOIN entities ON entities.id = edges.to_id \ + WHERE edges.kind = 'in_subsystem' \ + AND edges.from_id = ?1 \ + AND entities.kind = 'subsystem' \ + ORDER BY edges.to_id \ + LIMIT 1", + params![module_id], + |row| row.get(0), + ) + .optional() + .map_err(StorageError::from) +} + pub fn candidate_entities_for_unresolved_sites( conn: &Connection, sites: &[UnresolvedCallSiteRow], @@ -433,6 +673,17 @@ fn map_unresolved_call_site_row(row: &Row<'_>) -> rusqlite::Result) -> rusqlite::Result { + let raw_confidence: String = row.get(1)?; + Ok(ReferenceEdgeMatch { + neighbor_id: row.get(0)?, + confidence: parse_confidence(&raw_confidence)?, + source_file_id: row.get(2)?, + source_byte_start: row.get(3)?, + source_byte_end: row.get(4)?, + }) +} + fn candidate_entities_for_expr( conn: &Connection, callee_expr: &str, @@ -522,17 +773,20 @@ fn parse_confidence(raw: &str) -> rusqlite::Result { impl StoredCallEdge { fn candidate_ids(&self) -> BTreeSet { - self.properties_json - .as_deref() - .and_then(|raw| serde_json::from_str::(raw).ok()) - .and_then(|value| value.get("candidates").and_then(|c| c.as_array()).cloned()) - .into_iter() - .flatten() - .filter_map(|value| value.as_str().map(ToOwned::to_owned)) - .collect() + candidate_ids(self.properties_json.as_deref()) } } +fn candidate_ids(properties_json: Option<&str>) -> BTreeSet { + properties_json + .and_then(|raw| serde_json::from_str::(raw).ok()) + .and_then(|value| value.get("candidates").and_then(|c| c.as_array()).cloned()) + .into_iter() + .flatten() + .filter_map(|value| value.as_str().map(ToOwned::to_owned)) + .collect() +} + fn normalize_lexically(path: &Path) -> PathBuf { let mut normalized = PathBuf::new(); for component in path.components() { diff --git a/crates/clarion-storage/src/reader.rs b/crates/clarion-storage/src/reader.rs index b9cd5dbc..8856becc 100644 --- a/crates/clarion-storage/src/reader.rs +++ b/crates/clarion-storage/src/reader.rs @@ -42,8 +42,11 @@ impl ReaderPool { /// Acquire a reader and run a blocking closure on it. /// - /// Read-side PRAGMAs are applied on every acquisition — cheap and - /// guarantees `busy_timeout` + `foreign_keys` are always on. + /// Read-side PRAGMAs are applied on every acquisition even though they + /// persist for a connection's lifetime. This is an intentional + /// belt-and-suspenders choice: `deadpool-sqlite` opens connections lazily, + /// the current API does not install a post-create hook, and these two + /// PRAGMAs are cheap compared with the queries that use the reader. /// /// The closure must be `'static`: captures must be owned or cloned /// into the closure (borrowed references from the caller's scope diff --git a/crates/clarion-storage/src/schema.rs b/crates/clarion-storage/src/schema.rs index ed40a0c7..1a0adff6 100644 --- a/crates/clarion-storage/src/schema.rs +++ b/crates/clarion-storage/src/schema.rs @@ -114,5 +114,30 @@ pub fn applied_count(conn: &Connection) -> Result { let n: i64 = conn.query_row("SELECT COUNT(*) FROM schema_migrations", [], |row| { row.get(0) })?; - Ok(u32::try_from(n).unwrap_or(u32::MAX)) + migration_count_to_u32(n) +} + +fn migration_count_to_u32(n: i64) -> Result { + u32::try_from(n).map_err(|_| StorageError::Migration { + version: 0, + source: rusqlite::Error::IntegralValueOutOfRange(0, n), + }) +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn migration_count_conversion_rejects_overflow() { + let err = migration_count_to_u32(i64::from(u32::MAX) + 1) + .expect_err("overflowing migration count should error"); + assert!(matches!( + err, + StorageError::Migration { + version: 0, + source: rusqlite::Error::IntegralValueOutOfRange(0, _), + } + )); + } } diff --git a/crates/clarion-storage/src/writer.rs b/crates/clarion-storage/src/writer.rs index defb7eb5..73143ea3 100644 --- a/crates/clarion-storage/src/writer.rs +++ b/crates/clarion-storage/src/writer.rs @@ -24,8 +24,8 @@ use crate::cache::{ upsert_inferred_edge_cache, upsert_summary_cache, }; use crate::commands::{ - Ack, EdgeConfidence, EdgeRecord, EntityRecord, InferredCallEdgeRecord, InferredEdgeWriteStats, - RunStatus, WriterCmd, + Ack, EdgeConfidence, EdgeRecord, EntityRecord, FindingRecord, InferredCallEdgeRecord, + InferredEdgeWriteStats, RunStatus, WriterCmd, }; use crate::error::{Result, StorageError}; use crate::pragma; @@ -177,6 +177,14 @@ fn run_actor( ); reply(ack, res); } + WriterCmd::InsertFinding { finding, ack } => { + let res = insert_finding(conn, &mut state, &finding, commits_observed); + reply(ack, res); + } + WriterCmd::FlushRunBatch { ack } => { + let res = flush_run_batch(conn, &mut state, commits_observed); + reply(ack, res); + } WriterCmd::InsertInferredEdges { cache_entry, edges, @@ -248,13 +256,12 @@ fn run_actor( } } } - // Channel closed. Best-effort cleanup. - // - // Two hazards to cover: an open entity transaction must be rolled back, - // and — if a run was in progress — its `runs.status` row must not be - // left permanently as `'running'`. We self-heal both. This path is - // reached when the Writer handle is dropped mid-run; once the normal - // CommitRun / FailRun flows are used, current_run is None here. + cleanup_after_channel_close(conn, &mut state); +} + +fn cleanup_after_channel_close(conn: &mut Connection, state: &mut ActorState) { + // Two hazards to cover: an open entity transaction must be rolled back, and + // a run in progress must not be left permanently as `'running'`. if state.in_tx { let _ = conn.execute_batch("ROLLBACK"); state.in_tx = false; @@ -340,10 +347,12 @@ fn insert_entity( "InsertEntity received without a preceding BeginRun".to_owned(), )); } + enforce_entity_kind_contract(entity)?; if !state.in_tx { conn.execute_batch("BEGIN")?; state.in_tx = true; } + validate_entity_source_file_anchor(conn, entity)?; conn.execute( "INSERT INTO entities ( \ id, plugin_id, kind, name, short_name, \ @@ -389,6 +398,76 @@ fn insert_entity( Ok(()) } +fn enforce_entity_kind_contract(entity: &EntityRecord) -> Result<()> { + if entity.plugin_id != "core" + && clarion_core::plugin::manifest::RESERVED_ENTITY_KINDS.contains(&entity.kind.as_str()) + { + return Err(StorageError::WriterProtocol(format!( + "CLA-INFRA-RESERVED-ENTITY-KIND: entity kind {kind:?} is reserved by core; \ + plugin_id={plugin_id:?} cannot insert entity {id:?}", + kind = entity.kind, + plugin_id = entity.plugin_id, + id = entity.id, + ))); + } + Ok(()) +} + +// B.6 stores module ids as source anchors until core-minted `file` entities +// land; keep both accepted so the storage contract survives that handoff. +const SOURCE_FILE_ANCHOR_KINDS: &[&str] = &["file", "module"]; + +fn validate_source_file_anchor( + conn: &Connection, + source_file_id: Option<&str>, + context: &str, +) -> Result<()> { + let Some(source_file_id) = source_file_id else { + return Ok(()); + }; + let kind = conn + .query_row( + "SELECT kind FROM entities WHERE id = ?1", + params![source_file_id], + |row| row.get::<_, String>(0), + ) + .map_err(|err| match err { + rusqlite::Error::QueryReturnedNoRows => StorageError::WriterProtocol(format!( + "CLA-INFRA-SOURCE-FILE-MISSING: {context} {source_file_id:?} \ + does not reference an existing entity" + )), + other => StorageError::Sqlite(other), + })?; + if !SOURCE_FILE_ANCHOR_KINDS.contains(&kind.as_str()) { + let allowed = SOURCE_FILE_ANCHOR_KINDS; + return Err(StorageError::WriterProtocol(format!( + "CLA-INFRA-SOURCE-FILE-KIND-CONTRACT: {context} {source_file_id:?} \ + MUST reference a source-anchor entity with kind in {allowed:?}; \ + got kind={kind:?}" + ))); + } + Ok(()) +} + +fn validate_entity_source_file_anchor(conn: &Connection, entity: &EntityRecord) -> Result<()> { + let Some(source_file_id) = entity.source_file_id.as_deref() else { + return Ok(()); + }; + if source_file_id == entity.id { + if SOURCE_FILE_ANCHOR_KINDS.contains(&entity.kind.as_str()) { + return Ok(()); + } + let allowed = SOURCE_FILE_ANCHOR_KINDS; + return Err(StorageError::WriterProtocol(format!( + "CLA-INFRA-SOURCE-FILE-KIND-CONTRACT: InsertEntity source_file_id {source_file_id:?} \ + MUST reference a source-anchor entity with kind in {allowed:?}; \ + got kind={:?}", + entity.kind + ))); + } + validate_source_file_anchor(conn, Some(source_file_id), "InsertEntity source_file_id") +} + /// 9 ontology-defined edge kinds (ADR-026 + ADR-028). Unknown kinds reaching the /// writer are a manifest/wire-version drift bug — reject strictly. const STRUCTURAL_EDGE_KINDS: &[&str] = &["contains", "in_subsystem", "guides", "emits_finding"]; @@ -400,6 +479,13 @@ const ANCHORED_EDGE_KINDS: &[&str] = &[ "inherits_from", ]; +pub fn known_scan_time_edge_kinds() -> impl Iterator { + STRUCTURAL_EDGE_KINDS + .iter() + .chain(ANCHORED_EDGE_KINDS.iter()) + .copied() +} + /// Enforce the per-kind confidence + source-range contract documented in /// `docs/implementation/sprint-2/b3-contains-edges.md` §3 Q5 and ADR-026 /// decision 3, extended by ADR-028. Returns a @@ -492,6 +578,11 @@ fn insert_edge( conn.execute_batch("BEGIN")?; state.in_tx = true; } + validate_source_file_anchor( + conn, + edge.source_file_id.as_deref(), + "InsertEdge source_file_id", + )?; let changed = conn.execute( "INSERT OR IGNORE INTO edges ( \ kind, from_id, to_id, properties, source_file_id, \ @@ -519,6 +610,58 @@ fn insert_edge( Ok(()) } +fn insert_finding( + conn: &mut Connection, + state: &mut ActorState, + finding: &FindingRecord, + commits_observed: &AtomicUsize, +) -> Result<()> { + if state.current_run.is_none() { + return Err(StorageError::WriterProtocol( + "InsertFinding received without a preceding BeginRun".to_owned(), + )); + } + if !state.in_tx { + conn.execute_batch("BEGIN")?; + state.in_tx = true; + } + conn.execute( + "INSERT INTO findings ( \ + id, tool, tool_version, run_id, rule_id, kind, severity, confidence, \ + confidence_basis, entity_id, related_entities, message, evidence, \ + properties, supports, supported_by, status, suppression_reason, \ + filigree_issue_id, created_at, updated_at \ + ) VALUES ( \ + ?1, ?2, ?3, ?4, ?5, ?6, ?7, ?8, \ + ?9, ?10, ?11, ?12, ?13, \ + ?14, ?15, ?16, 'open', NULL, \ + NULL, ?17, ?18 \ + )", + params![ + finding.id, + finding.tool, + finding.tool_version, + finding.run_id, + finding.rule_id, + finding.kind, + finding.severity, + finding.confidence, + finding.confidence_basis, + finding.entity_id, + finding.related_entities_json, + finding.message, + finding.evidence_json, + finding.properties_json, + finding.supports_json, + finding.supported_by_json, + finding.created_at, + finding.updated_at, + ], + )?; + bump_writes_and_maybe_commit(conn, state, commits_observed)?; + Ok(()) +} + fn insert_inferred_edges( conn: &Connection, cache_entry: &InferredEdgeCacheEntry, @@ -541,6 +684,11 @@ fn insert_inferred_edges( }; for edge in edges { validate_inferred_edge(edge)?; + validate_source_file_anchor( + conn, + edge.source_file_id.as_deref(), + "InsertInferredEdges source_file_id", + )?; if static_call_edge_exists(conn, &edge.from_id, &edge.to_id)? { stats.skipped_static_duplicates += 1; continue; @@ -615,6 +763,13 @@ fn replace_unresolved_call_sites_in_run( conn.execute_batch("BEGIN")?; state.in_tx = true; } + for site in sites { + validate_source_file_anchor( + conn, + site.source_file_id.as_deref(), + "ReplaceUnresolvedCallSitesForCaller source_file_id", + )?; + } replace_unresolved_call_sites_for_caller(conn, caller_entity_id, caller_content_hash, sites)?; bump_writes_and_maybe_commit(conn, state, commits_observed)?; Ok(()) @@ -644,6 +799,35 @@ fn bump_writes_and_maybe_commit( Ok(()) } +fn flush_run_batch( + conn: &mut Connection, + state: &mut ActorState, + commits_observed: &AtomicUsize, +) -> Result<()> { + if state.current_run.is_none() { + return Err(StorageError::WriterProtocol( + "FlushRunBatch received without a preceding BeginRun".to_owned(), + )); + } + if let Some(mismatch) = parent_contains_mismatch(conn)? { + if state.in_tx { + let _ = conn.execute_batch("ROLLBACK"); + state.in_tx = false; + state.writes_in_batch = 0; + } + return Err(StorageError::WriterProtocol(mismatch)); + } + if state.in_tx { + state.in_tx = false; + state.writes_in_batch = 0; + conn.execute_batch("COMMIT")?; + commits_observed.fetch_add(1, Ordering::Relaxed); + } + conn.execute_batch("BEGIN")?; + state.in_tx = true; + Ok(()) +} + fn query_time_write( conn: &mut Connection, state: &mut ActorState, @@ -677,6 +861,7 @@ fn commit_run( stats_json: &str, commits_observed: &AtomicUsize, ) -> Result<()> { + ensure_current_run_matches(state, "CommitRun", run_id)?; // The run-row UPDATE and the final write-batch COMMIT must be atomic, // otherwise a crash or SQL error between them would leave entities/edges // durable but `runs.status = 'running'` — indistinguishable from an @@ -695,18 +880,29 @@ fn commit_run( "failure_reason": mismatch.clone(), }) .to_string(); - conn.execute( + let changed = conn.execute( "UPDATE runs SET status = 'failed', completed_at = ?1, stats = ?2 \ WHERE id = ?3", params![completed_at, failure_stats, run_id], )?; + if let Err(err) = ensure_run_update_changed_one(changed, run_id) { + state.current_run = None; + return Err(err); + } state.current_run = None; return Err(StorageError::WriterProtocol(mismatch)); } - conn.execute( + let changed = conn.execute( "UPDATE runs SET status = ?1, completed_at = ?2, stats = ?3 WHERE id = ?4", params![status.as_str(), completed_at, stats_json, run_id], )?; + if let Err(err) = ensure_run_update_changed_one(changed, run_id) { + let _ = conn.execute_batch("ROLLBACK"); + state.in_tx = false; + state.current_run = None; + state.writes_in_batch = 0; + return Err(err); + } state.in_tx = false; conn.execute_batch("COMMIT")?; commits_observed.fetch_add(1, Ordering::Relaxed); @@ -716,10 +912,15 @@ fn commit_run( // atomic under SQLite's implicit transaction. No entities/edges were // staged-and-not-committed, so the parent-id check has nothing to // catch that would change the durable state. - conn.execute( + let changed = conn.execute( "UPDATE runs SET status = ?1, completed_at = ?2, stats = ?3 WHERE id = ?4", params![status.as_str(), completed_at, stats_json, run_id], )?; + if let Err(err) = ensure_run_update_changed_one(changed, run_id) { + state.current_run = None; + state.writes_in_batch = 0; + return Err(err); + } } state.current_run = None; state.writes_in_batch = 0; @@ -802,16 +1003,48 @@ fn fail_run( reason: &str, completed_at: &str, ) -> Result<()> { + ensure_current_run_matches(state, "FailRun", run_id)?; if state.in_tx { let _ = conn.execute_batch("ROLLBACK"); state.in_tx = false; } let stats_json = serde_json::json!({ "failure_reason": reason }).to_string(); - conn.execute( + let changed = conn.execute( "UPDATE runs SET status = 'failed', completed_at = ?1, stats = ?2 WHERE id = ?3", params![completed_at, stats_json, run_id], )?; + if let Err(err) = ensure_run_update_changed_one(changed, run_id) { + state.current_run = None; + state.writes_in_batch = 0; + return Err(err); + } state.current_run = None; state.writes_in_batch = 0; Ok(()) } + +fn ensure_current_run_matches( + state: &ActorState, + command: &'static str, + run_id: &str, +) -> Result<()> { + match state.current_run.as_deref() { + Some(current) if current == run_id => Ok(()), + Some(current) => Err(StorageError::WriterProtocol(format!( + "{command} run_id={run_id:?} does not match active run_id={current:?}", + ))), + None => Err(StorageError::WriterProtocol(format!( + "{command} received without a preceding BeginRun", + ))), + } +} + +fn ensure_run_update_changed_one(changed: usize, run_id: &str) -> Result<()> { + if changed == 1 { + Ok(()) + } else { + Err(StorageError::WriterProtocol(format!( + "UPDATE runs affected {changed} rows for run_id={run_id}", + ))) + } +} diff --git a/crates/clarion-storage/tests/query_helpers.rs b/crates/clarion-storage/tests/query_helpers.rs index 5fb3b86a..d0c194aa 100644 --- a/crates/clarion-storage/tests/query_helpers.rs +++ b/crates/clarion-storage/tests/query_helpers.rs @@ -4,8 +4,10 @@ use std::path::Path; use clarion_core::EdgeConfidence; use clarion_storage::{ - call_edges_from, call_edges_targeting, child_entity_ids, contained_entity_ids, entity_at_line, - entity_by_id, find_entities, normalize_source_path, pragma, schema, + ModuleDependencyEdge, ReferenceDirection, SubsystemMember, call_edges_from, + call_edges_targeting, child_entity_ids, contained_entity_ids, entity_at_line, entity_by_id, + find_entities, module_dependency_edges, normalize_source_path, pragma, + reference_edges_for_entity, schema, subsystem_for_member, subsystem_members, }; use rusqlite::{Connection, params}; @@ -18,15 +20,27 @@ fn open_fresh(tempdir: &tempfile::TempDir) -> Connection { } fn insert_entity(conn: &Connection, id: &str, kind: &str) { + insert_named_entity(conn, id, kind, id, id, None); +} + +fn insert_named_entity( + conn: &Connection, + id: &str, + kind: &str, + name: &str, + short_name: &str, + source_file_path: Option<&str>, +) { conn.execute( "INSERT INTO entities ( - id, plugin_id, kind, name, short_name, properties, created_at, updated_at + id, plugin_id, kind, name, short_name, source_file_path, properties, created_at, + updated_at ) VALUES ( - ?1, 'python', ?2, ?1, ?1, '{}', + ?1, 'python', ?2, ?3, ?4, ?5, '{}', strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), strftime('%Y-%m-%dT%H:%M:%fZ', 'now') )", - params![id, kind], + params![id, kind, name, short_name, source_file_path], ) .expect("insert entity"); } @@ -89,6 +103,415 @@ fn insert_contains_edge(conn: &Connection, from_id: &str, to_id: &str) { .expect("insert contains edge"); } +fn insert_references_edge( + conn: &Connection, + from_id: &str, + to_id: &str, + confidence: EdgeConfidence, + start: i64, + end: i64, +) { + conn.execute( + "INSERT INTO edges ( + kind, from_id, to_id, confidence, source_byte_start, source_byte_end + ) VALUES ('references', ?1, ?2, ?3, ?4, ?5)", + params![from_id, to_id, confidence.as_str(), start, end], + ) + .expect("insert references edge"); +} + +fn insert_imports_edge(conn: &Connection, from_id: &str, to_id: &str) { + conn.execute( + "INSERT INTO edges ( + kind, from_id, to_id, confidence, source_byte_start, source_byte_end + ) VALUES ('imports', ?1, ?2, 'resolved', 30, 40)", + params![from_id, to_id], + ) + .expect("insert imports edge"); +} + +fn insert_in_subsystem_edge(conn: &Connection, module_id: &str, subsystem_id: &str) { + conn.execute( + "INSERT INTO edges (kind, from_id, to_id, confidence) + VALUES ('in_subsystem', ?1, ?2, 'resolved')", + params![module_id, subsystem_id], + ) + .expect("insert in_subsystem edge"); +} + +#[test] +fn module_dependency_edges_include_imports() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_entity(&conn, "python:module:pkg.alpha", "module"); + insert_entity(&conn, "python:module:pkg.beta", "module"); + insert_imports_edge(&conn, "python:module:pkg.alpha", "python:module:pkg.beta"); + + let edges = module_dependency_edges(&conn, &["imports"]).expect("module dependency edges"); + + assert_eq!( + edges, + vec![ModuleDependencyEdge { + from_module_id: "python:module:pkg.alpha".to_owned(), + to_module_id: "python:module:pkg.beta".to_owned(), + reference_count: 1, + edge_kinds: vec!["imports".to_owned()], + }], + ); +} + +#[test] +fn module_dependency_edges_roll_up_function_calls_to_parent_modules() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + for id in ["python:module:pkg.alpha", "python:module:pkg.beta"] { + insert_entity(&conn, id, "module"); + } + for id in [ + "python:function:pkg.alpha.source", + "python:function:pkg.beta.target", + ] { + insert_entity(&conn, id, "function"); + } + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.source", + ); + insert_contains_edge( + &conn, + "python:module:pkg.beta", + "python:function:pkg.beta.target", + ); + insert_calls_edge( + &conn, + "python:function:pkg.alpha.source", + "python:function:pkg.beta.target", + EdgeConfidence::Resolved, + &[], + ); + + let edges = module_dependency_edges(&conn, &["calls"]).expect("module dependency edges"); + + assert_eq!( + edges, + vec![ModuleDependencyEdge { + from_module_id: "python:module:pkg.alpha".to_owned(), + to_module_id: "python:module:pkg.beta".to_owned(), + reference_count: 1, + edge_kinds: vec!["calls".to_owned()], + }], + ); +} + +#[test] +fn module_dependency_edges_weight_by_reference_count() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + for id in ["python:module:pkg.alpha", "python:module:pkg.beta"] { + insert_entity(&conn, id, "module"); + } + for id in [ + "python:function:pkg.alpha.first", + "python:function:pkg.alpha.second", + "python:function:pkg.beta.target", + ] { + insert_entity(&conn, id, "function"); + } + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.first", + ); + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.second", + ); + insert_contains_edge( + &conn, + "python:module:pkg.beta", + "python:function:pkg.beta.target", + ); + insert_calls_edge( + &conn, + "python:function:pkg.alpha.first", + "python:function:pkg.beta.target", + EdgeConfidence::Resolved, + &[], + ); + insert_calls_edge( + &conn, + "python:function:pkg.alpha.second", + "python:function:pkg.beta.target", + EdgeConfidence::Resolved, + &[], + ); + insert_imports_edge(&conn, "python:module:pkg.alpha", "python:module:pkg.beta"); + + let edges = + module_dependency_edges(&conn, &["imports", "calls"]).expect("module dependency edges"); + + assert_eq!( + edges, + vec![ModuleDependencyEdge { + from_module_id: "python:module:pkg.alpha".to_owned(), + to_module_id: "python:module:pkg.beta".to_owned(), + reference_count: 3, + edge_kinds: vec!["calls".to_owned(), "imports".to_owned()], + }], + ); +} + +#[test] +fn module_dependency_edges_skip_self_edges() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_entity(&conn, "python:module:pkg.alpha", "module"); + insert_entity(&conn, "python:function:pkg.alpha.first", "function"); + insert_entity(&conn, "python:function:pkg.alpha.second", "function"); + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.first", + ); + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.second", + ); + insert_calls_edge( + &conn, + "python:function:pkg.alpha.first", + "python:function:pkg.alpha.second", + EdgeConfidence::Resolved, + &[], + ); + insert_imports_edge(&conn, "python:module:pkg.alpha", "python:module:pkg.alpha"); + + let edges = + module_dependency_edges(&conn, &["imports", "calls"]).expect("module dependency edges"); + + assert!(edges.is_empty()); +} + +#[test] +fn module_dependency_edges_exclude_inferred_calls() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + for id in ["python:module:pkg.alpha", "python:module:pkg.beta"] { + insert_entity(&conn, id, "module"); + } + for id in [ + "python:function:pkg.alpha.source", + "python:function:pkg.beta.target", + ] { + insert_entity(&conn, id, "function"); + } + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.source", + ); + insert_contains_edge( + &conn, + "python:module:pkg.beta", + "python:function:pkg.beta.target", + ); + insert_calls_edge( + &conn, + "python:function:pkg.alpha.source", + "python:function:pkg.beta.target", + EdgeConfidence::Inferred, + &[], + ); + + let edges = module_dependency_edges(&conn, &["calls"]).expect("module dependency edges"); + + assert!( + edges.is_empty(), + "query-time inferred calls must not contaminate Phase 3 clustering input" + ); +} + +#[test] +fn module_dependency_edges_expands_ambiguous_call_candidates() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + for id in [ + "python:module:pkg.alpha", + "python:module:pkg.beta", + "python:module:pkg.gamma", + ] { + insert_entity(&conn, id, "module"); + } + for id in [ + "python:function:pkg.alpha.source", + "python:function:pkg.beta.first", + "python:function:pkg.gamma.second", + ] { + insert_entity(&conn, id, "function"); + } + insert_contains_edge( + &conn, + "python:module:pkg.alpha", + "python:function:pkg.alpha.source", + ); + insert_contains_edge( + &conn, + "python:module:pkg.beta", + "python:function:pkg.beta.first", + ); + insert_contains_edge( + &conn, + "python:module:pkg.gamma", + "python:function:pkg.gamma.second", + ); + insert_calls_edge( + &conn, + "python:function:pkg.alpha.source", + "python:function:pkg.beta.first", + EdgeConfidence::Ambiguous, + &[ + "python:function:pkg.beta.first", + "python:function:pkg.gamma.second", + ], + ); + + let edges = module_dependency_edges(&conn, &["calls"]).expect("module dependency edges"); + + assert_eq!( + edges, + vec![ + ModuleDependencyEdge { + from_module_id: "python:module:pkg.alpha".to_owned(), + to_module_id: "python:module:pkg.beta".to_owned(), + reference_count: 1, + edge_kinds: vec!["calls".to_owned()], + }, + ModuleDependencyEdge { + from_module_id: "python:module:pkg.alpha".to_owned(), + to_module_id: "python:module:pkg.gamma".to_owned(), + reference_count: 1, + edge_kinds: vec!["calls".to_owned()], + }, + ], + ); +} + +#[test] +fn subsystem_members_returns_modules_ordered_by_name() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_named_entity( + &conn, + "core:subsystem:abc123def456", + "subsystem", + "Auth subsystem", + "Auth subsystem", + None, + ); + insert_named_entity( + &conn, + "python:module:pkg.beta", + "module", + "pkg.beta", + "beta", + Some("/tmp/pkg/beta.py"), + ); + insert_named_entity( + &conn, + "python:module:pkg.alpha", + "module", + "pkg.alpha", + "alpha", + Some("/tmp/pkg/alpha.py"), + ); + insert_in_subsystem_edge( + &conn, + "python:module:pkg.beta", + "core:subsystem:abc123def456", + ); + insert_in_subsystem_edge( + &conn, + "python:module:pkg.alpha", + "core:subsystem:abc123def456", + ); + + let members = + subsystem_members(&conn, "core:subsystem:abc123def456").expect("subsystem members"); + let subsystem = + subsystem_for_member(&conn, "python:module:pkg.alpha").expect("subsystem for member"); + + assert_eq!( + members, + vec![ + SubsystemMember { + id: "python:module:pkg.alpha".to_owned(), + name: "pkg.alpha".to_owned(), + source_file_path: Some("/tmp/pkg/alpha.py".to_owned()), + }, + SubsystemMember { + id: "python:module:pkg.beta".to_owned(), + name: "pkg.beta".to_owned(), + source_file_path: Some("/tmp/pkg/beta.py".to_owned()), + }, + ], + ); + assert_eq!(subsystem, Some("core:subsystem:abc123def456".to_owned())); + assert_eq!( + subsystem_for_member(&conn, "python:module:pkg.gamma").expect("unknown member"), + None, + ); +} + +#[test] +fn reference_edges_for_entity_returns_directional_neighbors() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_entity(&conn, "python:function:demo.source", "function"); + insert_entity(&conn, "python:function:demo.target", "function"); + insert_entity(&conn, "python:function:demo.outbound", "function"); + insert_references_edge( + &conn, + "python:function:demo.source", + "python:function:demo.target", + EdgeConfidence::Resolved, + 20, + 25, + ); + insert_references_edge( + &conn, + "python:function:demo.target", + "python:function:demo.outbound", + EdgeConfidence::Ambiguous, + 30, + 39, + ); + + let inbound = + reference_edges_for_entity(&conn, "python:function:demo.target", ReferenceDirection::In) + .expect("query inbound references"); + let outbound = reference_edges_for_entity( + &conn, + "python:function:demo.target", + ReferenceDirection::Out, + ) + .expect("query outbound references"); + + assert_eq!(inbound.len(), 1); + assert_eq!(inbound[0].neighbor_id, "python:function:demo.source"); + assert_eq!(inbound[0].confidence, EdgeConfidence::Resolved); + assert_eq!(inbound[0].source_byte_start, Some(20)); + assert_eq!(inbound[0].source_byte_end, Some(25)); + + assert_eq!(outbound.len(), 1); + assert_eq!(outbound[0].neighbor_id, "python:function:demo.outbound"); + assert_eq!(outbound[0].confidence, EdgeConfidence::Ambiguous); + assert_eq!(outbound[0].source_byte_start, Some(30)); + assert_eq!(outbound[0].source_byte_end, Some(39)); +} + #[test] fn call_edges_targeting_expands_candidate_only_ambiguous_targets() { let tempdir = tempfile::tempdir().unwrap(); diff --git a/crates/clarion-storage/tests/schema_apply.rs b/crates/clarion-storage/tests/schema_apply.rs index f1053f87..d29f0412 100644 --- a/crates/clarion-storage/tests/schema_apply.rs +++ b/crates/clarion-storage/tests/schema_apply.rs @@ -69,6 +69,22 @@ fn table_columns(conn: &Connection, table: &str) -> Vec { .collect() } +fn primary_key_columns(conn: &Connection, table: &str) -> Vec { + let mut stmt = conn + .prepare(&format!("PRAGMA table_info({table})")) + .unwrap(); + let mut columns = stmt + .query_map([], |row| { + Ok((row.get::<_, String>(1)?, row.get::<_, i64>(5)?)) + }) + .unwrap() + .map(std::result::Result::unwrap) + .filter(|(_, pk_position)| *pk_position > 0) + .collect::>(); + columns.sort_by_key(|(_, pk_position)| *pk_position); + columns.into_iter().map(|(name, _)| name).collect() +} + #[test] fn migration_0001_creates_every_expected_table() { let tempdir = tempfile::tempdir().unwrap(); @@ -92,6 +108,21 @@ fn migration_0001_creates_every_expected_table() { } } +#[test] +fn entity_tags_primary_key_includes_tag_owner_plugin() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + + assert_eq!( + table_columns(&conn, "entity_tags"), + ["entity_id", "plugin_id", "tag"] + ); + assert_eq!( + primary_key_columns(&conn, "entity_tags"), + ["entity_id", "plugin_id", "tag"] + ); +} + #[test] fn migration_0001_creates_entity_fts_virtual_table() { let tempdir = tempfile::tempdir().unwrap(); @@ -125,6 +156,41 @@ fn migration_0001_creates_entity_source_file_path_column_and_index() { ); } +#[test] +fn schema_accepts_open_entity_and_edge_kinds() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + + conn.execute( + "INSERT INTO entities ( + id, plugin_id, kind, name, short_name, properties, created_at, updated_at + ) VALUES ( + 'custom:widget:left', 'custom', 'widget', 'left', 'left', '{}', + strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), + strftime('%Y-%m-%dT%H:%M:%fZ', 'now') + )", + [], + ) + .expect("insert custom source entity kind"); + conn.execute( + "INSERT INTO entities ( + id, plugin_id, kind, name, short_name, properties, created_at, updated_at + ) VALUES ( + 'custom:gadget:right', 'custom', 'gadget', 'right', 'right', '{}', + strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), + strftime('%Y-%m-%dT%H:%M:%fZ', 'now') + )", + [], + ) + .expect("insert custom target entity kind"); + conn.execute( + "INSERT INTO edges (kind, from_id, to_id, confidence) + VALUES ('custom_relation', 'custom:widget:left', 'custom:gadget:right', 'resolved')", + [], + ) + .expect("insert custom edge kind"); +} + #[test] fn migration_0001_extends_summary_cache_for_mcp_staleness_tracking() { let tempdir = tempfile::tempdir().unwrap(); @@ -657,3 +723,179 @@ fn schema_migrations_records_one_row() { .unwrap(); assert_eq!(name, "0001_initial_schema"); } + +// ---------------------------------------------------------------------------- +// ADR-031: schema-validation policy. Each CHECK-constrained enum-shaped TEXT +// column must reject out-of-vocabulary inserts at the SQL layer. These tests +// mirror `edges_confidence_column_rejects_unknown_tier` (line 538) and serve +// as the executable record of the closed-vocabulary policy. +// ---------------------------------------------------------------------------- + +fn insert_anchor_entity(conn: &Connection, id: &str) { + conn.execute( + "INSERT INTO entities (id, plugin_id, kind, name, short_name, properties, \ + created_at, updated_at) \ + VALUES (?1, 'python', 'function', ?1, ?1, '{}', \ + strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), strftime('%Y-%m-%dT%H:%M:%fZ', 'now'))", + params![id], + ) + .unwrap(); +} + +fn insert_run(conn: &Connection, id: &str) { + conn.execute( + "INSERT INTO runs (id, started_at, config, stats, status) \ + VALUES (?1, strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), '{}', '{}', 'running')", + params![id], + ) + .unwrap(); +} + +fn insert_finding( + conn: &Connection, + entity_id: &str, + kind: &str, + severity: &str, + status: &str, +) -> rusqlite::Result { + conn.execute( + "INSERT INTO findings (id, tool, tool_version, run_id, rule_id, kind, severity, \ + entity_id, related_entities, message, evidence, properties, supports, \ + supported_by, status, created_at, updated_at) \ + VALUES ('f1', 'clarion', '0.1', 'r1', 'CLA-FACT-TODO', ?1, ?2, ?3, '[]', \ + 'm', '{}', '{}', '[]', '[]', ?4, \ + strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), strftime('%Y-%m-%dT%H:%M:%fZ', 'now'))", + params![kind, severity, entity_id, status], + ) +} + +#[test] +fn findings_run_id_rejects_missing_run() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_anchor_entity(&conn, "python:function:demo.a"); + let err = insert_finding(&conn, "python:function:demo.a", "fact", "INFO", "open") + .expect_err("findings.run_id should reference an existing run"); + assert!( + err.to_string().contains("FOREIGN KEY constraint failed"), + "unexpected error for missing run_id: {err}" + ); +} + +#[test] +fn findings_kind_check_rejects_unknown_value() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_run(&conn, "r1"); + insert_anchor_entity(&conn, "python:function:demo.a"); + let err = insert_finding(&conn, "python:function:demo.a", "bogus", "INFO", "open") + .expect_err("findings.kind CHECK should reject unknown values"); + assert!( + err.to_string().contains("CHECK constraint failed"), + "unexpected error for invalid kind: {err}" + ); +} + +#[test] +fn findings_kind_check_accepts_all_documented_values() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_run(&conn, "r1"); + insert_anchor_entity(&conn, "python:function:demo.a"); + // Insert each documented kind in turn; deletion between iterations keeps + // the PRIMARY KEY available. + for kind in ["defect", "fact", "classification", "metric", "suggestion"] { + insert_finding(&conn, "python:function:demo.a", kind, "INFO", "open") + .unwrap_or_else(|err| panic!("kind={kind} rejected unexpectedly: {err}")); + conn.execute("DELETE FROM findings", []).unwrap(); + } +} + +#[test] +fn findings_severity_check_rejects_unknown_value() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_run(&conn, "r1"); + insert_anchor_entity(&conn, "python:function:demo.a"); + let err = insert_finding(&conn, "python:function:demo.a", "fact", "info", "open") + .expect_err("findings.severity CHECK should reject lowercase 'info'"); + assert!( + err.to_string().contains("CHECK constraint failed"), + "unexpected error for invalid severity: {err}" + ); +} + +#[test] +fn findings_severity_check_accepts_all_documented_values() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_run(&conn, "r1"); + insert_anchor_entity(&conn, "python:function:demo.a"); + for severity in ["INFO", "WARN", "ERROR", "CRITICAL", "NONE"] { + insert_finding(&conn, "python:function:demo.a", "fact", severity, "open") + .unwrap_or_else(|err| panic!("severity={severity} rejected unexpectedly: {err}")); + conn.execute("DELETE FROM findings", []).unwrap(); + } +} + +#[test] +fn findings_status_check_rejects_unknown_value() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_run(&conn, "r1"); + insert_anchor_entity(&conn, "python:function:demo.a"); + let err = insert_finding(&conn, "python:function:demo.a", "fact", "INFO", "closed") + .expect_err("findings.status CHECK should reject 'closed'"); + assert!( + err.to_string().contains("CHECK constraint failed"), + "unexpected error for invalid status: {err}" + ); +} + +#[test] +fn findings_status_check_accepts_all_documented_values() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + insert_run(&conn, "r1"); + insert_anchor_entity(&conn, "python:function:demo.a"); + for status in ["open", "acknowledged", "suppressed", "promoted_to_issue"] { + insert_finding(&conn, "python:function:demo.a", "fact", "INFO", status) + .unwrap_or_else(|err| panic!("status={status} rejected unexpectedly: {err}")); + conn.execute("DELETE FROM findings", []).unwrap(); + } +} + +#[test] +fn runs_status_check_rejects_unknown_value() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + let err = conn + .execute( + "INSERT INTO runs (id, started_at, config, stats, status) \ + VALUES ('r1', strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), '{}', '{}', 'runing')", + [], + ) + .expect_err("runs.status CHECK should reject 'runing' typo"); + assert!( + err.to_string().contains("CHECK constraint failed"), + "unexpected error for invalid runs.status: {err}" + ); +} + +#[test] +fn runs_status_check_accepts_all_documented_values() { + let tempdir = tempfile::tempdir().unwrap(); + let conn = open_fresh(&tempdir); + for (i, status) in ["running", "skipped_no_plugins", "completed", "failed"] + .iter() + .enumerate() + { + let id = format!("r{i}"); + conn.execute( + "INSERT INTO runs (id, started_at, config, stats, status) \ + VALUES (?1, strftime('%Y-%m-%dT%H:%M:%fZ', 'now'), '{}', '{}', ?2)", + params![id, status], + ) + .unwrap_or_else(|err| panic!("runs.status={status} rejected unexpectedly: {err}")); + } +} diff --git a/crates/clarion-storage/tests/writer_actor.rs b/crates/clarion-storage/tests/writer_actor.rs index c2e43e55..9fe9eb56 100644 --- a/crates/clarion-storage/tests/writer_actor.rs +++ b/crates/clarion-storage/tests/writer_actor.rs @@ -10,7 +10,7 @@ use tokio::sync::oneshot; use clarion_storage::{ InferredCallEdgeRecord, InferredEdgeCacheEntry, InferredEdgeCacheKey, ReaderPool, SummaryCacheEntry, SummaryCacheKey, UnresolvedCallSiteRecord, Writer, - commands::{EdgeConfidence, EdgeRecord, EntityRecord, RunStatus, WriterCmd}, + commands::{EdgeConfidence, EdgeRecord, EntityRecord, FindingRecord, RunStatus, WriterCmd}, pragma, schema, }; @@ -542,6 +542,270 @@ async fn round_trip_insert_persists_entity() { assert_eq!(kind, "function"); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn non_core_plugin_cannot_insert_reserved_entity_kind() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + send::<()>(&tx, |ack| WriterCmd::BeginRun { + run_id: "run-reserved-kind".into(), + config_json: "{}".into(), + started_at: now_iso(), + ack, + }) + .await + .unwrap(); + + let mut reserved = make_entity("python:subsystem:demo"); + reserved.kind = "subsystem".to_owned(); + + let result = send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(reserved), + ack, + }) + .await; + + if result.is_ok() { + send::<()>(&tx, |ack| WriterCmd::FailRun { + run_id: "run-reserved-kind".into(), + completed_at: now_iso(), + reason: "test cleanup".into(), + ack, + }) + .await + .unwrap(); + } + + let err = result.expect_err("reserved entity kind from non-core plugin must fail"); + assert!( + matches!(err, clarion_storage::StorageError::WriterProtocol(_)), + "expected WriterProtocol, got {err:?}" + ); + assert!( + err.to_string().contains("CLA-INFRA-RESERVED-ENTITY-KIND"), + "error should carry reserved-kind code; got {err:#}" + ); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); + + let pool = ReaderPool::open(&path, 2).unwrap(); + let entity_count: i64 = pool + .with_reader(|conn| { + let n: i64 = conn.query_row("SELECT COUNT(*) FROM entities", [], |row| row.get(0))?; + Ok(n) + }) + .await + .unwrap(); + assert_eq!(entity_count, 0); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn writer_inserts_fact_findings() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + begin_demo_run(&tx, "run-finding").await; + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_module_entity("python:module:demo")), + ack, + }) + .await + .unwrap(); + + send::<()>(&tx, |ack| WriterCmd::InsertFinding { + finding: Box::new(FindingRecord { + id: "finding-1".to_owned(), + tool: "clarion".to_owned(), + tool_version: "0.1.0".to_owned(), + run_id: "run-finding".to_owned(), + rule_id: "CLA-FACT-CLUSTERING-WEAK-MODULARITY".to_owned(), + kind: "fact".to_owned(), + severity: "INFO".to_owned(), + confidence: Some(0.9), + confidence_basis: Some("deterministic modularity calculation".to_owned()), + entity_id: "python:module:demo".to_owned(), + related_entities_json: r#"["python:module:demo"]"#.to_owned(), + message: "Module graph has weak subsystem modularity".to_owned(), + evidence_json: r#"{"modularity_score":0.0}"#.to_owned(), + properties_json: r#"{"threshold":0.25}"#.to_owned(), + supports_json: "[]".to_owned(), + supported_by_json: "[]".to_owned(), + created_at: now_iso(), + updated_at: now_iso(), + }), + ack, + }) + .await + .unwrap(); + + send::<()>(&tx, |ack| WriterCmd::CommitRun { + run_id: "run-finding".into(), + status: RunStatus::Completed, + completed_at: now_iso(), + stats_json: "{}".into(), + ack, + }) + .await + .unwrap(); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); + + let conn = Connection::open(path).unwrap(); + let row: ( + String, + String, + String, + String, + String, + String, + String, + String, + String, + ) = conn + .query_row( + "SELECT rule_id, kind, severity, status, related_entities, evidence, properties, \ + supports, supported_by FROM findings WHERE id = ?1", + rusqlite::params!["finding-1"], + |row| { + Ok(( + row.get(0)?, + row.get(1)?, + row.get(2)?, + row.get(3)?, + row.get(4)?, + row.get(5)?, + row.get(6)?, + row.get(7)?, + row.get(8)?, + )) + }, + ) + .unwrap(); + assert_eq!( + row, + ( + "CLA-FACT-CLUSTERING-WEAK-MODULARITY".to_owned(), + "fact".to_owned(), + "INFO".to_owned(), + "open".to_owned(), + r#"["python:module:demo"]"#.to_owned(), + r#"{"modularity_score":0.0}"#.to_owned(), + r#"{"threshold":0.25}"#.to_owned(), + "[]".to_owned(), + "[]".to_owned(), + ) + ); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn entity_source_file_id_rejects_non_source_anchor_entity() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + begin_demo_run(&tx, "run-source-anchor").await; + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_module_entity("python:module:demo")), + ack, + }) + .await + .unwrap(); + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_entity_with_parent( + "python:function:demo.source_like_but_not_file", + Some("python:module:demo"), + )), + ack, + }) + .await + .unwrap(); + + let mut bad = make_entity_with_parent( + "python:function:demo.bad_source_anchor", + Some("python:module:demo"), + ); + bad.source_file_id = Some("python:function:demo.source_like_but_not_file".to_owned()); + + let result = send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(bad), + ack, + }) + .await; + let err = result.expect_err("source_file_id must point at a source-anchor entity"); + assert!( + format!("{err:?}").contains("CLA-INFRA-SOURCE-FILE-KIND-CONTRACT"), + "expected CLA-INFRA-SOURCE-FILE-KIND-CONTRACT in error; got {err:?}" + ); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn module_entity_may_reference_itself_as_source_file_id() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + begin_demo_run(&tx, "run-source-self").await; + + let mut module = make_module_entity("python:module:demo"); + module.source_file_id = Some("python:module:demo".to_owned()); + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(module), + ack, + }) + .await + .expect("module source anchor may reference itself"); + + send::<()>(&tx, |ack| WriterCmd::CommitRun { + run_id: "run-source-self".into(), + status: RunStatus::Completed, + completed_at: now_iso(), + stats_json: "{}".into(), + ack, + }) + .await + .unwrap(); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); +} + +#[test] +fn python_plugin_edge_kinds_are_accepted_by_writer_contract() { + let manifest = + clarion_core::parse_manifest(include_bytes!("../../../plugins/python/plugin.toml")) + .expect("production Python plugin manifest should parse"); + let writer_kinds: std::collections::BTreeSet<&'static str> = + clarion_storage::known_scan_time_edge_kinds().collect(); + let missing: Vec<&str> = manifest + .ontology + .edge_kinds + .iter() + .map(String::as_str) + .filter(|kind| !writer_kinds.contains(kind)) + .collect(); + + assert!( + missing.is_empty(), + "Python plugin declares edge kind(s) the writer rejects: {missing:?}; \ + writer accepts {writer_kinds:?}" + ); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn batch_size_fifty_commits_every_fifty_inserts() { let dir = tempfile::tempdir().unwrap(); @@ -597,6 +861,69 @@ async fn batch_size_fifty_commits_every_fifty_inserts() { assert_eq!(count, 150); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn cloned_senders_accept_concurrent_entity_producers() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + begin_demo_run(&tx, "run-concurrent-producers").await; + + let tx_a = tx.clone(); + let producer_a = tokio::spawn(async move { + for i in 0..25 { + let id = format!("python:function:demo.producer_a_{i:02}"); + send::<()>(&tx_a, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_entity(&id)), + ack, + }) + .await + .unwrap(); + } + }); + let tx_b = tx.clone(); + let producer_b = tokio::spawn(async move { + for i in 0..25 { + let id = format!("python:function:demo.producer_b_{i:02}"); + send::<()>(&tx_b, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_entity(&id)), + ack, + }) + .await + .unwrap(); + } + }); + producer_a.await.unwrap(); + producer_b.await.unwrap(); + + assert_eq!(writer.commits_observed.load(Ordering::Relaxed), 1); + + send::<()>(&tx, |ack| WriterCmd::CommitRun { + run_id: "run-concurrent-producers".into(), + status: RunStatus::Completed, + completed_at: now_iso(), + stats_json: "{}".into(), + ack, + }) + .await + .unwrap(); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); + + let pool = ReaderPool::open(&path, 2).unwrap(); + let count: i64 = pool + .with_reader(|conn| { + let n: i64 = conn.query_row("SELECT COUNT(*) FROM entities", [], |row| row.get(0))?; + Ok(n) + }) + .await + .unwrap(); + assert_eq!(count, 50); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn fail_run_rolls_back_pending_inserts() { let dir = tempfile::tempdir().unwrap(); @@ -659,6 +986,68 @@ async fn fail_run_rolls_back_pending_inserts() { assert_eq!(status, "failed"); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn fail_run_after_prior_batch_commit_rolls_back_only_pending_inserts() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + send::<()>(&tx, |ack| WriterCmd::BeginRun { + run_id: "run-fail-after-batch".into(), + config_json: "{}".into(), + started_at: now_iso(), + ack, + }) + .await + .unwrap(); + + for i in 0..60 { + let id = format!("python:function:demo.batch_fail_{i:03}"); + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_entity(&id)), + ack, + }) + .await + .unwrap(); + } + + assert_eq!(writer.commits_observed.load(Ordering::Relaxed), 1); + + send::<()>(&tx, |ack| WriterCmd::FailRun { + run_id: "run-fail-after-batch".into(), + reason: "deliberate test failure".into(), + completed_at: now_iso(), + ack, + }) + .await + .unwrap(); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); + + let pool = ReaderPool::open(&path, 2).unwrap(); + let (entity_count, status): (i64, String) = pool + .with_reader(|conn| { + let n: i64 = conn.query_row("SELECT COUNT(*) FROM entities", [], |row| row.get(0))?; + let s: String = conn.query_row( + "SELECT status FROM runs WHERE id = 'run-fail-after-batch'", + [], + |row| row.get(0), + )?; + Ok((n, s)) + }) + .await + .unwrap(); + + assert_eq!( + entity_count, 50, + "FailRun must preserve prior committed batches and roll back only the open batch" + ); + assert_eq!(status, "failed"); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn insert_entity_without_begin_run_is_protocol_violation() { let dir = tempfile::tempdir().unwrap(); @@ -683,6 +1072,132 @@ async fn insert_entity_without_begin_run_is_protocol_violation() { handle.await.unwrap().unwrap(); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn commit_run_without_begin_run_is_protocol_violation() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + let result = send::<()>(&tx, |ack| WriterCmd::CommitRun { + run_id: "run-cold".into(), + status: RunStatus::Completed, + completed_at: now_iso(), + stats_json: "{}".into(), + ack, + }) + .await; + + let err = result.expect_err("CommitRun without BeginRun should fail"); + assert!( + matches!(err, clarion_storage::StorageError::WriterProtocol(_)), + "expected WriterProtocol, got {err:?}" + ); + assert!( + err.to_string().contains("without a preceding BeginRun"), + "error should explain missing BeginRun: {err}" + ); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn fail_run_without_begin_run_is_protocol_violation() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + let result = send::<()>(&tx, |ack| WriterCmd::FailRun { + run_id: "run-cold".into(), + reason: "test".into(), + completed_at: now_iso(), + ack, + }) + .await; + + let err = result.expect_err("FailRun without BeginRun should fail"); + assert!( + matches!(err, clarion_storage::StorageError::WriterProtocol(_)), + "expected WriterProtocol, got {err:?}" + ); + assert!( + err.to_string().contains("without a preceding BeginRun"), + "error should explain missing BeginRun: {err}" + ); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn commit_run_with_stale_run_id_is_protocol_violation() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + begin_demo_run(&tx, "run-active").await; + + let result = send::<()>(&tx, |ack| WriterCmd::CommitRun { + run_id: "run-stale".into(), + status: RunStatus::Completed, + completed_at: now_iso(), + stats_json: "{}".into(), + ack, + }) + .await; + + let err = result.expect_err("stale CommitRun run_id should fail"); + assert!( + matches!(err, clarion_storage::StorageError::WriterProtocol(_)), + "expected WriterProtocol, got {err:?}" + ); + assert!( + err.to_string().contains("run-stale"), + "error should name stale run id: {err}" + ); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); +} + +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn fail_run_with_stale_run_id_is_protocol_violation() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + begin_demo_run(&tx, "run-active").await; + + let result = send::<()>(&tx, |ack| WriterCmd::FailRun { + run_id: "run-stale".into(), + reason: "test".into(), + completed_at: now_iso(), + ack, + }) + .await; + + let err = result.expect_err("stale FailRun run_id should fail"); + assert!( + matches!(err, clarion_storage::StorageError::WriterProtocol(_)), + "expected WriterProtocol, got {err:?}" + ); + assert!( + err.to_string().contains("run-stale"), + "error should name stale run id: {err}" + ); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn double_begin_run_is_protocol_violation() { let dir = tempfile::tempdir().unwrap(); @@ -1175,6 +1690,77 @@ async fn orphan_contains_edge_with_no_matching_parent_id_rejects_run() { handle.await.unwrap().unwrap(); } +#[tokio::test(flavor = "multi_thread", worker_threads = 2)] +async fn flush_run_batch_rejects_parent_contains_mismatch_before_commit() { + let dir = tempfile::tempdir().unwrap(); + let path = prepared_db(&dir); + let (writer, handle) = Writer::spawn(path.clone(), 50, 256).unwrap(); + let tx = writer.sender(); + + send::<()>(&tx, |ack| WriterCmd::BeginRun { + run_id: "run-flush-mismatch".into(), + config_json: "{}".into(), + started_at: now_iso(), + ack, + }) + .await + .unwrap(); + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_module_entity("python:module:demo")), + ack, + }) + .await + .unwrap(); + send::<()>(&tx, |ack| WriterCmd::InsertEntity { + entity: Box::new(make_entity_with_parent( + "python:function:demo.lonely", + Some("python:module:demo"), + )), + ack, + }) + .await + .unwrap(); + + let result = send::<()>(&tx, |ack| WriterCmd::FlushRunBatch { ack }).await; + let err = result.expect_err("FlushRunBatch should reject parent mismatch"); + assert!( + format!("{err:?}").contains("CLA-INFRA-PARENT-CONTAINS-MISMATCH"), + "expected CLA-INFRA-PARENT-CONTAINS-MISMATCH in error; got {err:?}" + ); + + send::<()>(&tx, |ack| WriterCmd::FailRun { + run_id: "run-flush-mismatch".into(), + reason: "phase3 clustering failed: parent mismatch".into(), + completed_at: now_iso(), + ack, + }) + .await + .unwrap(); + + drop(tx); + drop(writer); + handle.await.unwrap().unwrap(); + + let pool = ReaderPool::open(&path, 1).unwrap(); + let (status, entity_count): (String, i64) = pool + .with_reader(|conn| { + let s: String = conn.query_row( + "SELECT status FROM runs WHERE id = 'run-flush-mismatch'", + [], + |row| row.get(0), + )?; + let n: i64 = conn.query_row("SELECT COUNT(*) FROM entities", [], |row| row.get(0))?; + Ok((s, n)) + }) + .await + .unwrap(); + assert_eq!(status, "failed"); + assert_eq!( + entity_count, 0, + "flush-boundary rejection must roll back pending plugin rows" + ); +} + #[tokio::test(flavor = "multi_thread", worker_threads = 2)] async fn writes_in_batch_counts_entities_and_edges_uniformly() { // Q2 / Task 2: rename inserts_in_batch -> writes_in_batch and increment @@ -1691,7 +2277,7 @@ async fn channel_close_with_open_run_self_heals_to_failed() { // The run row must have been self-healed to 'failed'. The pending insert // is rolled back. let pool = ReaderPool::open(&path, 1).expect("pool"); - let (observed_status, observed_reason, entity_count): (String, String, i64) = pool + let (run_status, stats_json, entity_count): (String, String, i64) = pool .with_reader(|conn| { let (s, st): (String, String) = conn.query_row( "SELECT status, stats FROM runs WHERE id = 'run-abandoned'", @@ -1705,12 +2291,14 @@ async fn channel_close_with_open_run_self_heals_to_failed() { .expect("reader query"); assert_eq!( - observed_status, "failed", + run_status, "failed", "self-heal must mark abandoned run as failed" ); - assert!( - observed_reason.contains("writer channel closed unexpectedly"), - "failure_reason must cite channel close; got stats = {observed_reason}" + let stats: serde_json::Value = + serde_json::from_str(&stats_json).expect("stats must be valid JSON"); + assert_eq!( + stats["failure_reason"], "writer channel closed unexpectedly", + "failure_reason must cite channel close; got stats = {stats_json}" ); assert_eq!( entity_count, 0, diff --git a/docs/arch-analysis-2026-05-18-1244/00-coordination.md b/docs/arch-analysis-2026-05-18-1244/00-coordination.md new file mode 100644 index 00000000..cb4fa9b6 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/00-coordination.md @@ -0,0 +1,50 @@ +# Analysis Coordination Plan + +## Configuration + +- **Scope**: Full repo (`crates/`, `plugins/`, `tests/`, `fixtures/`, `docs/`) +- **Deliverables**: **Option A — Full Analysis** (auto-selected per user "no clarifying questions" directive; user explicitly asked for a "detailed report") + - `01-discovery-findings.md` + - `02-subsystem-catalog.md` + - `03-diagrams.md` + - `04-final-report.md` +- **Strategy**: **PARALLEL** (6 candidate subsystems, loosely coupled along crate boundaries) +- **Tier**: MEDIUM (~30k LOC, 6 subsystem candidates, well below ultralarge thresholds) +- **Time constraint**: None stated +- **Complexity estimate**: Medium — well-documented codebase with ADRs, REQ IDs, and recent sprint sign-offs to cross-check against findings + +## Subsystem candidates (pre-discovery hypothesis) + +1. `clarion-core` — entity-ID assembler, plugin host, JSON-RPC transport, jail/limits +2. `clarion-storage` — writer-actor + reader-pool over SQLite (ADR-011) +3. `clarion-cli` — `clarion` binary (`install`, `analyze`) +4. `clarion-mcp` — MCP server (Sprint-2 work, new since Sprint-1 docs were written) +5. `clarion-plugin-fixture` — test-only fixture plugin +6. `plugins/python` — Python language plugin (JSON-RPC peer) + +`tests/e2e` and `fixtures/` are cross-cutting; will be folded into the relevant subsystems. + +## Execution log + +- 2026-05-18 12:44 — Created workspace +- 2026-05-18 12:44 — Auto-selected Option A (no-clarifying-questions directive in force) +- 2026-05-18 12:44 — Scale assessed: 24 462 Rust + 5 629 Python LOC, 5 crates + 1 plugin → MEDIUM tier, PARALLEL strategy +- 2026-05-18 12:49 — `01-discovery-findings.md` written by `codebase-explorer` (384 lines) +- 2026-05-18 12:51 — Dispatched 5 parallel `codebase-explorer` agents (one per subsystem; fixture folded into Python plugin pass) +- 2026-05-18 12:55 — All 5 section files received (clarion-core, clarion-storage, clarion-mcp, clarion-cli, python plugin + fixture) +- 2026-05-18 13:00 — `02-subsystem-catalog.md` assembled (648 lines including index + footnotes) +- 2026-05-18 13:00 — Validation gate spawned (`analysis-validator`) → NEEDS_REVISION (warnings); one factual contradiction (fixture/clarion-core dep) corrected in-place, footnote added for LOC drift +- 2026-05-18 13:03 — `03-diagrams.md` written by coordinator using Mermaid Chart MCP validator for syntax checks; 5 diagrams (Context, Container, analyze sequence, MCP summary sequence, plugin-host component) +- 2026-05-18 13:06 — Validation gate spawned for diagrams → APPROVED +- 2026-05-18 13:10 — `04-final-report.md` written by coordinator (synthesis layer) +- 2026-05-18 13:13 — Validation gate spawned for final report → NEEDS_REVISION (warnings); 5 stale numeric facts (LOC + commit count + diff stat + one line number + WP count) corrected in-place; commit hash `363bb0a` pinned in report header +- 2026-05-18 13:14 — Workflow complete; all deliverables in workspace + +## Outcomes + +| Deliverable | Status | +|---|---| +| `01-discovery-findings.md` | Written (single-explorer pass, no validation gate required) | +| `02-subsystem-catalog.md` | Validated NEEDS_REVISION (warnings) → corrections applied | +| `03-diagrams.md` | Validated APPROVED | +| `04-final-report.md` | Validated NEEDS_REVISION (warnings) → corrections applied; commit hash pinned | diff --git a/docs/arch-analysis-2026-05-18-1244/01-discovery-findings.md b/docs/arch-analysis-2026-05-18-1244/01-discovery-findings.md new file mode 100644 index 00000000..30fbca6a --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/01-discovery-findings.md @@ -0,0 +1,384 @@ +# 01 — Discovery Findings + +**Repository:** `/home/john/clarion` +**Branch:** `sprint-2/b8-scale-test` (11 commits ahead of `main`) +**Tags present:** `v0.1-sprint-1`, `v0.1-sprint-2` +**Discovery pass run:** 2026-05-18 +**Methodology:** SME Agent Protocol — metadata → structure → routers → sampling → quantitative. No depth-reads on sibling-subsystem files; that's the next pass. + +--- + +## 1. Repository organisation + +### 1.1 Top-level layout (Confidence: High — `ls /home/john/clarion`) + +``` +/home/john/clarion +├── Cargo.toml workspace root (5-member virtual workspace) +├── Cargo.lock +├── CLAUDE.md project doctrine + filigree workflow +├── rust-toolchain.toml +├── rustfmt.toml +├── clippy.toml +├── deny.toml cargo-deny config (ADR-023 floor) +├── crates/ 5 Rust crates (workspace members) +├── plugins/python/ Python plugin (installed via `pip install -e plugins/python[dev]`) +├── tests/ cross-crate e2e + perf harnesses +│ ├── e2e/ two bash scripts: Sprint-1 walking skeleton + Sprint-2 MCP surface +│ └── perf/ B.5 reference-scale smoke + B.8 scale-test harness + result snapshots +├── fixtures/ single file — `entity_id.json` (cross-language L2 parity proof) +├── scripts/ (not deep-read in this pass) +├── docs/ doctrine + design + ADRs + implementation plans (79 .md files) +└── target/ cargo build artifacts (gitignored) +``` + +### 1.2 Organisation principle (Confidence: High — `Cargo.toml` workspace + crate-name semantics) + +Clarion is organised as a **plugin-extensible monolith with a layered Rust core**: + +- **Layer-by-crate**: `clarion-core` (domain types + plugin host) → `clarion-storage` (SQLite persistence) → `clarion-mcp` (read surface) → `clarion-cli` (binary glue). The CLI depends transitively on every other crate; `clarion-mcp` and `clarion-storage` depend on `clarion-core`; `clarion-storage` does not depend on `clarion-mcp`. No circular references at the crate level. +- **Plugin-extensible**: language plugins are *out-of-process subprocesses* spoken to over Content-Length-framed JSON-RPC. `crates/clarion-plugin-fixture/` is a Rust test plugin; `plugins/python/` is the real Python plugin. This is enforced by ADR-021 (plugin authority — hybrid) and ADR-022 (core/plugin ontology ownership). +- **Per-product documentation**: `docs/clarion/` is product-scoped; `docs/suite/` is Loom-federation-scoped; `docs/implementation/sprint-{1,2}/` is execution-scoped. No documentation lives next to source modules. + +The principle "the core never invents kinds" (ADR-022) is the load-bearing organisational rule: the plugin owns segment 1 (plugin_id) and segment 3 (canonical qualified name) of every entity ID; the core owns segment 2 (kind) only at the schema level. + +--- + +## 2. Technology stack + +### 2.1 Rust toolchain (Confidence: High — `rust-toolchain.toml` + `Cargo.toml`) + +- **Edition**: 2024 (workspace-wide) +- **MSRV**: 1.85 (`Cargo.toml:8`) +- **Resolver**: 3 +- **Lint floor** (workspace lints, `Cargo.toml:13–22`): + - `unsafe_code = "deny"` (downgraded from `forbid` per documented exception: `CommandExt::pre_exec` calling `setrlimit(2)` in the forked plugin child) + - `clippy::pedantic = warn` at `priority = -1`, with three pragmatic allows: `module_name_repetitions`, `must_use_candidate`, `missing_errors_doc` + +### 2.2 Workspace dependencies (Confidence: High — `Cargo.toml` `[workspace.dependencies]`) + +Heavy hitters by responsibility: + +- **Async runtime**: `tokio 1` (`rt-multi-thread, macros, sync, time`) +- **Storage**: `rusqlite 0.31` (bundled), `deadpool-sqlite 0.8` (reader pool per ADR-011) +- **HTTP**: `reqwest 0.12` (blocking + JSON + `rustls-tls-native-roots`; no native OpenSSL) +- **Serialisation**: `serde 1`, `serde_json 1`, `toml 0.8`, `serde_norway 0.9` (YAML — replaces unsound `serde_yaml`, see commit `9ffc5c8`) +- **CLI / errors**: `clap 4` (derive), `anyhow 1`, `thiserror 1` +- **Hashing / IDs**: `blake3 1.8.5`, `uuid 1` (v4) +- **Observability**: `tracing 0.1` + `tracing-subscriber 0.3` (`env-filter`) +- **POSIX limits**: `nix 0.28` (`resource` feature only) — used by `apply_prlimit_as` / `apply_prlimit_nofile_nproc` +- **Configuration helper**: `dotenvy 0.15` (loaded in `main.rs` before tracing init) +- **Test scaffolding**: `assert_cmd 2`, `tempfile 3` + +### 2.3 Python plugin toolchain (Confidence: High — `plugins/python/pyproject.toml`) + +- **Build backend**: `hatchling` +- **Python**: `>=3.11`, targets 3.11 + 3.12 +- **Runtime deps** (intentionally tiny — the plugin is a stdlib-first ast walker): + - `packaging>=24` — version-range comparison for Wardline pin + - `pyright==1.1.409` — pinned exact-version for cross-reference resolution (`pyright_session.py`, the largest Python file at 1251 lines) +- **Dev deps**: `pytest 8+`, `pytest-cov 5+`, `ruff 0.6+`, `mypy 1.11+`, `pre-commit 3.8+` +- **Lint/format/typecheck**: `ruff select = ["ALL"]` with pragmatic ignores (D, COM812, ISC001, CPY, ANN401, TRY003); `mypy --strict`; `max-complexity = 15` to match Rust clippy +- **Script entry**: `clarion-plugin-python = "clarion_plugin_python.__main__:main"` +- **Manifest packaging**: hatch shared-data routes `plugin.toml` → `share/clarion/plugins/python/plugin.toml` so the core's L9 PATH discovery finds it. + +### 2.4 Plugin manifest (`plugins/python/plugin.toml`) + +The plugin declares its capabilities at install time (Confidence: High — full file read): + +- `plugin_id = "python"`, `protocol_version = "1.0"` +- `expected_max_rss_mb = 2048` (clamped against core 2 GiB ceiling per ADR-021 §2b) +- `expected_entities_per_file = 5000` +- `wardline_aware = true`, `reads_outside_project_root = false` +- `[ontology] entity_kinds = ["function", "class", "module"]`, `edge_kinds = ["contains", "calls", "references"]`, `ontology_version = "0.5.0"` (B.5* MINOR bump per ADR-027) +- `rule_id_prefix = "CLA-PY-"` (ADR-022 grammar) +- Wardline pin: `min_version = "1.0.0", max_version = "2.0.0"` + +--- + +## 3. Entry points + +### 3.1 Single binary: `clarion` (Confidence: High — `crates/clarion-cli/src/main.rs:1–25`) + +```rust +match cli.command { + Command::Install { force, path } => install::run(&path, force), + Command::Analyze { path } => block_on(analyze::run(path)), + Command::Serve { path, config } => serve::run(&path, config.as_deref()), +} +``` + +Three CLI subcommands (`crates/clarion-cli/src/cli.rs:1–45`): + +- `clarion install [--path PATH] [--force]` — initialise `.clarion/clarion.db` against the current schema migration. +- `clarion analyze [PATH]` — discover plugins via L9 `$PATH` convention, walk source tree, spawn plugin processes, persist entities/edges via writer-actor. +- `clarion serve [--path PATH] [--config PATH]` — **new in Sprint 2** — run the MCP stdio server (`serve.rs:1–90`). Reads `clarion.yaml`, wires the LLM provider (OpenRouter, Recording, or disabled), wires the optional Filigree HTTP client, and dispatches to `clarion_mcp::serve_stdio_with_state_on_runtime`. + +A `.env` file is loaded from CWD or any ancestor *before* tracing init (commit `dc9bf41`); existing process env vars win per dotenvy default. + +### 3.2 Plugin process entry: `clarion-plugin-python` + +`plugins/python/src/clarion_plugin_python/__main__.py` (15 lines, all of it shown): + +```python +from clarion_plugin_python.server import main +if __name__ == "__main__": + sys.exit(main()) +``` + +`server.py` (285 lines) speaks the L4 five-method JSON-RPC protocol: `initialize`, `initialized`, `analyze_file`, `shutdown`, `exit`. `MAX_CONTENT_LENGTH = 8 MiB` matches the host's ADR-021 §2b ceiling. `stdout_guard.py` (62 lines) replaces stdout with a strict transport channel so stray `print()` cannot corrupt the wire. + +### 3.3 Test fixture plugin: `clarion-plugin-fixture` + +`crates/clarion-plugin-fixture/src/main.rs` (128 lines) — Rust binary that speaks the same L4 protocol as the Python plugin; consumed only by `wp2_e2e` integration tests. + +### 3.4 Integration-test entry points + +- `tests/e2e/sprint_1_walking_skeleton.sh` — runs the README §3 demo verbatim; asserts SQLite returns Python module/function entities, source ranges, content hashes, and resolved+ambiguous call edges and references. +- `tests/e2e/sprint_2_mcp_surface.sh` — exists (not deep-read this pass); presumably exercises the seven MCP tools. +- `tests/perf/b8_scale_test/driver.py` — 816-line scale-test harness against the `elspeth` corpus (and `tests/perf/elspeth_mini/`). + +--- + +## 4. Subsystem identification + +The 6-candidate hypothesis is **confirmed**. Refined per crate evidence below. + +### Subsystem A — `clarion-core` (~3 100 LOC actual code, 10 686 LOC including tests) + +- **Location**: `crates/clarion-core/src/` +- **One-sentence responsibility**: Owns the canonical entity-ID format, the plugin host (subprocess supervisor + JSON-RPC peer), the LLM-provider abstraction, and the jail/limits ceilings that all other crates use. +- **Primary modules** (Confidence: High — `ls` + per-file LOC): + - `entity_id.rs` (610 LOC) — three-segment ID assembler (`{plugin_id}:{kind}:{canonical_qualified_name}`); cross-validated against `fixtures/entity_id.json` (L2 parity proof). + - `llm_provider.rs` (948 LOC) — `LlmProvider` trait, `OpenRouterProvider`, `RecordingProvider` (test-mode), prompt templates for leaf-summary and inferred-calls (`LEAF_SUMMARY_PROMPT_TEMPLATE_ID`, `INFERRED_CALLS_PROMPT_VERSION`). + - `plugin/` submodule (~7 400 LOC across 9 files): + - `host.rs` (3126 LOC) — supervisor; the single largest file in the codebase + - `manifest.rs` (1508 LOC) — `plugin.toml` parser + validator (ADR-021/ADR-022) + - `protocol.rs` (846 LOC) — JSON-RPC 2.0 typed envelopes + - `mock.rs` (897 LOC, `#[cfg(test)]`) — in-process mock plugin for unit tests + - `discovery.rs` (637 LOC) — `$PATH` scanning for `clarion-plugin-*` executables + - `transport.rs` (568 LOC) — Content-Length framing + - `limits.rs` (552 LOC) — entity-cap, frame-oversize, RSS, prlimit application + - `breaker.rs` (360 LOC) — crash-loop circuit breaker (ADR-002 §UQ-WP2-10) + - `jail.rs` (253 LOC) — path-jail enforcement (ADR-021 §2a) +- **External interface**: Rust-only — re-exports a curated facade through `lib.rs` (47 lines; see commit `ticket clarion-29acbcd042` policy note). Implementation types stay accessible via `clarion_core::plugin::transport::*` and siblings. + +### Subsystem B — `clarion-storage` (~1 950 LOC actual code, 5 453 LOC with tests) + +- **Location**: `crates/clarion-storage/src/` +- **One-sentence responsibility**: Writer-actor + reader-pool over a single SQLite database at `.clarion/clarion.db`, with all writes funnelled through one `tokio::task` per ADR-011. +- **Modules**: + - `writer.rs` (817 LOC) — writer-actor command loop; owns the sole write `rusqlite::Connection`; enforces edge contract (`enforce_edge_contract`, called out at `writer.rs:411` in ADR-031). + - `query.rs` (569 LOC) — read-side helpers for MCP tools (graph navigation: `call_edges_from`, `contained_entity_ids`, `entity_at_line`, `find_entities`, etc.). + - `commands.rs` (183 LOC) — `WriterCmd`, `EntityRecord`, `EdgeRecord`, `InferredCallEdgeRecord`, `RunStatus` — typed enums at the command boundary. + - `cache.rs` (251 LOC) — `SummaryCacheKey` (5-tuple per ADR-007), `InferredEdgeCacheKey`, `summary_cache_lookup`, `inferred_edge_cache_lookup`. + - `unresolved.rs` (50 LOC) — unresolved call-site bookkeeping (B.4*). + - `schema.rs` (118 LOC) — migration runner. + - `pragma.rs` (45 LOC) — PRAGMA block (WAL, busy_timeout, etc.). + - `reader.rs` (88 LOC) — `deadpool-sqlite` pool wrapper. + - `error.rs` (48 LOC) — `StorageError` taxonomy. +- **Schema**: single migration at `crates/clarion-storage/migrations/0001_initial_schema.sql` (289 lines). Per the migration's own comment block, the file is edit-in-place under ADR-024 until an external operator builds a `.clarion/clarion.db` from a published build. The 2026-05-18 edits added `CHECK` constraints on closed core-owned vocabularies (`findings.{kind,severity,status}`, `runs.status`) per ADR-031; `entities.kind` and `edges.kind` deliberately do *not* gain CHECKs because their vocabularies are plugin-extensible. +- **External interface**: `WriterCmd` enum + `ReaderPool` + query helpers, exposed via `lib.rs` re-exports (40 LOC). + +### Subsystem C — `clarion-mcp` (~3 200 LOC actual code, 4 917 LOC with tests) — *Sprint-2 new* + +- **Location**: `crates/clarion-mcp/src/` +- **One-sentence responsibility**: Speaks MCP protocol revision `2025-11-25` over stdio; serves seven storage-backed read tools to consult-mode LLM agents; integrates the LLM provider for on-demand summaries and inferred call edges; integrates Filigree as an enrichment source. +- **Modules**: + - `lib.rs` (2617 LOC) — `ServerState`, tool dispatch, the seven `ToolDefinition`s, dispatch glue to `clarion-storage` query helpers and `clarion-core::LlmProvider`. Massive single file; could plausibly subdivide. + - `config.rs` (352 LOC) — `McpConfig`, `LlmConfig`, `ProviderSelection`, `select_provider_with_env`. YAML via `serde_norway` (the safe `serde_yaml` replacement). + - `filigree.rs` (238 LOC) — `FiligreeHttpClient`, `EntityAssociation`, `EntityAssociationsResponse`, `FiligreeLookup` trait (allows mocking). +- **Seven tools** (from `lib.rs::list_tools`): + 1. `entity_at` — innermost entity containing (file, line) + 2. `find_entity` — FTS search on id/name/short_name/summary + 3. `callers_of` — incoming call edges; default confidence `resolved` + 4. `execution_paths_from` — bounded calls-only paths; max_depth ≤ 8, default 3 + 5. `summary` — on-demand cached leaf summary (ADR-030 narrows to leaf scope for v0.1) + 6. `issues_for` — Filigree enrichment (enrich-only per Loom doctrine; unavailable envelope on Filigree downtime) + 7. `neighborhood` — one-hop graph view (callers, callees, container, contained, references) +- **External interface**: MCP stdio protocol; consumed by LLM agent clients via `clarion serve`. + +### Subsystem D — `clarion-cli` (~1 740 LOC actual code, 3 275 LOC with tests) + +- **Location**: `crates/clarion-cli/src/` +- **One-sentence responsibility**: Glue binary; `clap`-driven subcommand dispatch (`install`, `analyze`, `serve`) wiring `clarion-core` (plugin host) + `clarion-storage` (writer-actor + pool) + `clarion-mcp` (server). +- **Modules**: + - `main.rs` (33 LOC) — entrypoint; loads `.env`, parses CLI, dispatches. + - `cli.rs` (45 LOC) — `clap` derive structs. + - `analyze.rs` (1436 LOC) — orchestrates plugin discovery, source-tree walk, plugin handshake, per-file dispatch, writer-actor flushing, crash-loop accounting, error mapping to `FailRun` vs `SkippedNoPlugins`. + - `serve.rs` (136 LOC) — MCP server wiring (LLM provider build, Filigree client build, runtime + reader pool + writer wiring, stdio loop). + - `install.rs` (168 LOC) — `.clarion/` bootstrap + migration apply. + - `stats.rs` (small) — `P95Accumulator` helper for analyze-time latency reporting. +- **Integration tests** (`crates/clarion-cli/tests/`): + - `install.rs`, `analyze.rs`, `serve.rs` — per-subcommand black-box tests via `assert_cmd`. + - `wp1_e2e.rs`, `wp2_e2e.rs` — WP-level walking-skeleton tests; `wp2_e2e` consumes the `clarion-plugin-fixture` binary on disk. + +### Subsystem E — `clarion-plugin-fixture` (131 LOC, 2 source files) + +- **Location**: `crates/clarion-plugin-fixture/src/` +- **One-sentence responsibility**: Test-only Rust plugin speaking the L4 protocol; lets WP2 tests verify the host without bringing Python into the loop. +- **Modules**: `main.rs` (128 LOC) — full process entry; `lib.rs` (3 LOC) — re-export shim. +- **External interface**: stdin/stdout JSON-RPC, identical to Python plugin. + +### Subsystem F — `plugins/python` (Python plugin, 2670 LOC) + +- **Location**: `plugins/python/src/clarion_plugin_python/` +- **One-sentence responsibility**: Python language plugin — extracts module/class/function entities and `contains` + `calls` + `references` edges from a Python source tree; uses `pyright-langserver` for cross-reference resolution; speaks L4 JSON-RPC to the Rust host. +- **Modules** (by size): + - `pyright_session.py` (1251 LOC) — long-running `pyright-langserver` LSP client; the heaviest single file. + - `extractor.py` (744 LOC) — AST-based entity extraction; **modified on this branch** (+98 LOC, B.8 `@overload`-stub deduplication fix). + - `server.py` (285 LOC) — JSON-RPC dispatch loop. + - `entity_id.py` (75 LOC) — cross-language entity-ID assembler (parity-tested against `fixtures/entity_id.json`). + - `reference_resolver.py` (69 LOC) — references-edge collection (B.5*). + - `call_resolver.py` (64 LOC) — calls-edge resolution (B.4*). + - `stdout_guard.py` (62 LOC) — keeps stray prints off the wire. + - `wardline_probe.py` (56 LOC) — L8 Wardline-presence probe, reported in handshake `capabilities`. + - `qualname.py` (46 LOC) — Python-flavoured canonical qualname per ADR-018. + - `__main__.py` (15 LOC) / `__init__.py` (3 LOC). +- **External interface**: stdin/stdout JSON-RPC, console-script `clarion-plugin-python` on `$PATH`, manifest at `share/clarion/plugins/python/plugin.toml`. + +--- + +## 5. Cross-cutting concerns + +(Confidence: High where ADRs back the claim; Medium where inferred from imports.) + +- **Entity-ID format** — ADR-003 + ADR-022. Three colon-segments. Cross-validated by `fixtures/entity_id.json` against both the Rust `entity_id.rs` (610 LOC) and Python `entity_id.py` (75 LOC). This is the L2 byte-for-byte parity proof. +- **JSON-RPC L4 protocol** — ADR-002 + commit `b0a12a6`. Content-Length framing, five methods (`initialize`, `initialized`, `analyze_file`, `shutdown`, `exit`), 8 MiB cap on both sides. Speakers: `clarion-core::plugin::transport`, `clarion-plugin-fixture` main, `clarion-plugin-python::server`. +- **Ontology version semver** — ADR-027. Plugin manifest's `[ontology].ontology_version` follows MAJOR/MINOR/PATCH; B.5* was a MINOR bump (additive `references` edge kind) to `0.5.0`. +- **Edge confidence tiers** — ADR-028. `resolved` / `ambiguous` / `inferred`. MCP queries default to `>= resolved`; inferred edges are computed lazily at query time via LLM dispatch. +- **Summary cache key** — ADR-007. 5-tuple: (entity_id, content_hash, prompt_template_id, model_tier, guidance_fingerprint). `ontology_version` is explicitly NOT a cache-key component (it's handshake-validation only). +- **Loom federation doctrine** — `docs/suite/loom.md` §3–§5. Solo-useful + pairwise-composable + enrich-only. Two named v0.1 asterisks survive: Wardline→Filigree pipeline coupling via Clarion; Python plugin's `wardline.core.registry.REGISTRY` import. +- **Tooling baseline (ADR-023)** — `cargo fmt`, `cargo clippy -D warnings`, `cargo nextest`, `RUSTDOCFLAGS="-D warnings" cargo doc`, `cargo deny check`; ruff + ruff-format + mypy --strict + pytest. CI at `.github/workflows/ci.yml` has three jobs: `rust`, `python-plugin`, `walking-skeleton` (the last depends on the first two). +- **Schema-validation policy (ADR-031, NEW 2026-05-18)** — `CHECK` constraints required on closed core-owned TEXT-enum columns, forbidden on plugin-extensible ones. Writer-actor remains the canonical validator; CHECK is defense-in-depth. + +--- + +## 6. Documentation surface + +(Confidence: High — `find docs -name '*.md'` returned 79 files; full file paths inventoried but not deep-read.) + +### 6.1 Suite-level doctrine (`docs/suite/`, 4 files) + +- `loom.md` — federation axiom, §3–§5 are load-bearing +- `briefing.md` — 5-minute intro +- `glossary.md` — cross-product term registry (gate for ADR acceptance) +- `README.md` + +### 6.2 Clarion product docs (`docs/clarion/`) + +- `v0.1/requirements.md` — REQ-/NFR-/CON-/NG- baselined IDs +- `v0.1/system-design.md` — §2–§11 each with `Addresses:` headers naming requirement IDs +- `v0.1/detailed-design.md` — schemas, rule catalogues, appendices (modified on this branch, +15 lines) +- `v0.1/plans/v0.1-scope-commitments.md` — pre-implementation scope memo +- `v0.1/reviews/` — `panel-2026-04-17/` (4 files) + `pre-restructure/` (2 files). Supporting context, not normative. + +### 6.3 ADRs (`docs/clarion/adr/`, 25 Accepted + 1 README) + +Authored ADRs span 001–031 with gaps (008–010, 019–020 are tracked as backlog inside system-design §12 / detailed-design §11). All Accepted. ADR-031 was added on this branch (2026-05-18). + +### 6.4 Implementation plans (`docs/implementation/`) + +- `v0.1-plan.md` — 11 work packages in dependency order +- `sprint-1/` — `README.md`, `signoffs.md`, `wp1-scaffold.md`, `wp2-plugin-host.md`, `wp3-python-plugin.md` (closed at `v0.1-sprint-1`) +- `sprint-2/` — 12 files covering B.2, B.3, B.4*, B.5*, B.6, B.7, B.8 design + results + signoffs + OpenRouter swap memo + scope amendment memo. Sprint 2 closed at `v0.1-sprint-2` (initially RED on B.8, now GREEN after repair rerun captured in `b8-results.md`). + +### 6.5 Operator docs (`docs/operator/`, 2 files) + +- `README.md` + `openrouter.md` (provider-swap operator guide) + +### 6.6 Handoffs (`docs/superpowers/`, 11 files) + +8 dated handoff memos + 3 sprint plans. The most recent (`2026-05-16-sprint-2-resume.md`, `2026-05-03-skeleton-audit.md`) are the live carryover into the current branch. + +### 6.7 Top-level + +`docs/README.md` + `docs/clarion/README.md` + `docs/clarion/v0.1/README.md` + `docs/implementation/README.md` form the navigation tree. + +--- + +## 7. What's changed since Sprint 1 + +(Confidence: High — `git log --oneline v0.1-sprint-1..HEAD` + `git diff --stat main..HEAD`.) + +### 7.1 Whole-of-sprint-2 deltas (commits since `v0.1-sprint-1`) + +A **new top-level crate (`clarion-mcp`)** plus heavy growth in `clarion-cli` (the `serve` subcommand), `clarion-storage` (graph query helpers, LLM cache tables, unresolved call sites, source ranges), and the Python plugin (calls + references edges). Notable commit chains: + +- **B.2 (class + module entities)** — `e53191d` merge +- **B.3 (contains edges, first edge kind)** — `f9bd31e` merge, ontology `0.3.0` +- **B.4* (calls edges + confidence tiers)** — `837d965` merge, ontology `0.4.0` +- **B.5* (references edges via pyright)** — `e988a83` merge, ontology `0.5.0` +- **B.6 (seven-tool MCP surface)** — `ed64a16` merge, including `b0a12a6` (scaffold), `7c13b73` (`clarion serve`), `8b8ecdc` (graph query helpers), `7f6a51f` (storage-backed tools), `e964118` (MCP/LLM config), `5a9f218` (LLM cache tables), `6fba66b` (WP6 LLM provider surface), `5627686` (on-demand summary tool), `5dc6e23` (unresolved call sites), `dcf6a30` (inferred call-edge dispatch), `16634ae` (Filigree association contract test), `29d3865` (`issues_for`), `5588ed8` (full-surface e2e), `d1ebca4` (LLM budget reserve), `9ffc5c8` (replace unsound YAML parser → `serde_norway`), `fa5b7cb` (wire MCP LLM paths) +- **OpenRouter provider swap** — `35be4db` merge, `4af69fd` (replace Anthropic with OpenRouter), `a53d2e4` (operator docs), `ab6b1dd` (strict-JSON path for B.8 green rerun) +- **B.8 scale test** — `5a396a5` (plan + harness), `80a6af9` (heavy-sample steady-state), `ad2ef80` (RED results), `b87bc1d` (GREEN rerun on full elspeth), `ffdfd79` (signoff revised to GREEN) +- **Sprint hygiene** — `a80c31a` (gitignore `.env`), `dc9bf41` (load `.env` before tracing), `29f0426` (skip `@overload` stubs to prevent UNIQUE collision), `c7ec1dd` (ADR-031 CHECK clauses), `0cb61b4` (manifest rule-ID grammar fix) + +### 7.2 Current-branch (`sprint-2/b8-scale-test`) deltas against `main` (11 commits) + +`git diff --stat main..HEAD` shows 45 files changed, 23 209 insertions, 59 deletions. Substantive non-result-data changes: + +- **`crates/clarion-core/src/llm_provider.rs`** — +193 lines (OpenRouter strict-JSON path) +- **`crates/clarion-core/src/plugin/manifest.rs`** — +10 lines (ADR-022 rule-ID quantifier fix) +- **`crates/clarion-mcp/src/lib.rs`** — +171 lines (B.8 follow-up) +- **`crates/clarion-mcp/tests/storage_tools.rs`** — +184 lines +- **`crates/clarion-storage/migrations/0001_initial_schema.sql`** — +33 lines (ADR-031 CHECK clauses) +- **`crates/clarion-storage/tests/schema_apply.rs`** — +148 lines (new test verifying CHECK enforcement) +- **`docs/clarion/adr/ADR-031-schema-validation-policy.md`** — +426 lines (new ADR) +- **`plugins/python/src/clarion_plugin_python/extractor.py`** — +98 lines (`@overload`-stub skip) +- **`plugins/python/tests/test_extractor.py`** — +184 lines + +The bulk of the +23 209 line delta is **B.8 scale-test result artifacts** (`tests/perf/b8_scale_test/results/*/mcp-driver-output*.json`) — JSON drivers' captured outputs from the elspeth corpus run, plus the 816-line `driver.py` and 227-line `test_driver.py` harness. These are checked-in evidence, not source code. + +### 7.3 Working tree (not yet committed) + +`git status` shows 7 modified files + 1 new file (`docs/clarion/adr/ADR-031-schema-validation-policy.md`) + the result snapshot `tests/perf/b8_scale_test/results/2026-05-18T0017Z/`. The B.8 GREEN rerun results are partially committed and partially still in the working tree. + +--- + +## 8. Open questions for the deeper per-subsystem pass + +1. **`clarion-mcp/src/lib.rs` is 2 617 LOC in one file.** Is this a single coherent concern (tool dispatch) or a god-file that subdivides? The subsystem-catalog pass should examine internal structure — is there a `ServerState` impl, a per-tool handler set, and a transport loop, all in one file? If so, refactor candidates may surface. +2. **`clarion-core/src/plugin/host.rs` is 3 126 LOC.** Same question — supervisor logic vs handshake vs analyze-file orchestration. Sprint-1 lock-ins anchor this; understand which. +3. **`clarion-mcp` ↔ `clarion-storage` coupling.** `clarion-mcp::lib.rs` imports ~20 symbols from `clarion-storage` (`CallEdgeMatch`, `EntityRow`, `InferredCallEdgeRecord`, `ReaderPool`, etc.). Is the MCP layer a thin dispatch over storage query helpers, or does it also marshal/transform substantially? This affects the catalog's responsibility statement for `clarion-storage::query`. +4. **LLM-provider dispatch path.** `serve.rs` wires `OpenRouterProvider` | `RecordingProvider` | disabled. `dcf6a30` and `5627686` added inferred-edge and summary dispatch. The catalog pass should confirm what's actually cached vs lazy-computed and where the 5-tuple cache key is materialised (writer.rs vs lib.rs vs cache.rs). +5. **Filigree integration shape.** `filigree.rs` is 238 LOC; `issues_for` exists; ADR-029 governs the binding contract. The catalog should verify the "enrich-only" axiom is upheld at the code level — does any code path on the Clarion side *require* a Filigree response to succeed? +6. **Schema migration governance.** Single migration file (289 LOC), edit-in-place per ADR-024 until an external operator ships a published build. Currently three documented edit events (initial, 2026-05-03 ADR-024 rename, 2026-05-18 ADR-031 CHECKs). When does the retirement trigger fire? Catalog should record current state. +7. **`tests/perf/elspeth_mini/`** is a 3-file corpus checked in for harness self-tests. Confirm this is fixture data (not Clarion source); none of the discovery reads suggest it's wired into the build. +8. **Sprint-1 deferred items** (per `CLAUDE.md`) — six WP2 items, four WP1 review-2 P2 bugs, one WP9 amendment — are these still open Filigree issues, or has Sprint 2 closed some? The catalog pass may want to map deferred items to current crate state. + +--- + +## Confidence summary + +| Section | Confidence | Evidence | +|---|---|---| +| §1 Repository organisation | High | `ls` + `Cargo.toml` workspace members + ADR-022 | +| §2 Technology stack | High | `Cargo.toml`, `pyproject.toml`, `plugin.toml` read in full | +| §3 Entry points | High | `main.rs`, `cli.rs`, `__main__.py`, `serve.rs` read | +| §4 Subsystem identification | High for crate boundaries, Medium for "responsibility" claims (lib.rs facades read, internal implementations sampled by size only) | per-crate `src/` listings, `lib.rs` heads read, LOC counts per file | +| §5 Cross-cutting concerns | High where ADR-cited; Medium where inferred | ADR index, ADR-031, ADR-027, ADR-028, ADR-007 read | +| §6 Documentation surface | High (inventory only; no depth reads) | `find docs -name '*.md'` | +| §7 Sprint-2 deltas | High | `git log v0.1-sprint-1..HEAD`, `git diff --stat main..HEAD`, `git status` | +| §8 Open questions | N/A (questions, not findings) | n/a | + +--- + +## Risk Assessment + +- **Risk: file-size god-files** — Two source files exceed 2 600 LOC (`clarion-core/src/plugin/host.rs` 3126, `clarion-mcp/src/lib.rs` 2617). Catalog pass needs to confirm whether internal structure makes them coherent or whether they should be flagged for refactoring. +- **Risk: discovery undercounts plugin-side complexity** — `pyright_session.py` is 1 251 LOC of LSP-client logic; this is single-file in the plugin but represents a substantial dependency on an external process. The catalog pass for subsystem F must give this its own treatment. +- **Risk: Sprint-2 docs not yet fully inventoried** — 12 sprint-2 .md files exist; only `signoffs.md` was read in any depth this pass. The deeper pass should at least skim each B.* design doc for subsystem-level claims. + +## Information Gaps + +- LLM-provider dispatch internals (how the 5-tuple cache key is constructed and where the LRU/TTL logic lives). +- Whether `tests/e2e/sprint_2_mcp_surface.sh` actually executes all seven MCP tools or a subset. +- The `scripts/` directory contents (not enumerated this pass). +- Wardline / Filigree sibling-repo source — none of this is vendored; cross-product claims rely on doctrine + manifest pins only. + +## Caveats + +- LOC numbers include test code unless explicitly stated. The "actual code" subtotals exclude `tests/` subdirectories but include `#[cfg(test)]` modules in `src/` (e.g., `mock.rs` 897 LOC counts in `clarion-core`). +- This pass cited line ranges from file heads only; deeper file scrutiny is deferred to the per-subsystem catalog pass. +- No assessment of code *quality* is made here. That is a `axiom-system-architect:assess-architecture` concern, not a discovery concern. diff --git a/docs/arch-analysis-2026-05-18-1244/02-subsystem-catalog.md b/docs/arch-analysis-2026-05-18-1244/02-subsystem-catalog.md new file mode 100644 index 00000000..efeea122 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/02-subsystem-catalog.md @@ -0,0 +1,648 @@ +# 02 — Subsystem Catalog + +**Repository:** `/home/john/clarion` +**Branch:** `sprint-2/b8-scale-test` +**Catalog assembled:** 2026-05-18 + +This catalog documents the six subsystems identified in `01-discovery-findings.md` §4. Each entry was produced by a dedicated `axiom-system-archaeologist:codebase-explorer` subagent reading the crate's source in depth. Entries cite file:line throughout. + +## Subsystem index + +| # | Subsystem | Location | Production LOC (approx) | Inbound deps | Outbound (workspace) | +|---|---|---|---|---|---| +| A | `clarion-core` | `crates/clarion-core/` | ~3 100 | storage, mcp, cli | (none) | +| B | `clarion-storage` | `crates/clarion-storage/` | ~1 950 | mcp, cli | core (one symbol) | +| C | `clarion-mcp` | `crates/clarion-mcp/` | ~3 200 | cli | core, storage | +| D | `clarion-cli` | `crates/clarion-cli/` | ~1 740 | (binary — none) | core, storage, mcp | +| E | `clarion-plugin-fixture` | `crates/clarion-plugin-fixture/` | 131 | core (test only) | core (types only) | +| F | Python plugin | `plugins/python/src/clarion_plugin_python/` | ~2 670 | (subprocess of host) | pyright, packaging, wardline (soft) | + +Crate-level graph is acyclic (verified by cross-grep of `use clarion_*::` and `Cargo.toml` deps in each subagent's pass). The Python plugin is *not* a Rust crate; the only "dep" relationship is the host-spawns-subprocess contract. + +> **Footnotes on the index:** "Inbound deps" lists library-link consumers only — Cargo `[dev-dependencies]` are excluded. `clarion-cli` declares `clarion-plugin-fixture` under `[dev-dependencies]` for its `wp2_e2e` tests but does not link it in the production binary. LOC ranges throughout this catalog reflect the working tree at `sprint-2/b8-scale-test` HEAD on 2026-05-18; `clarion-mcp/src/lib.rs` is 2 623 lines as of this commit (a few entries below quote the immediate-pre-B.8 figure of 2 620 — drift of +3 lines from late-B.8 follow-up). + +--- + +## clarion-core + +**Location:** `crates/clarion-core/` + +**Responsibility:** Owns the canonical entity-ID grammar, plugin-host subprocess supervisor + JSON-RPC peer, LLM-provider trait + OpenRouter implementation, plugin-manifest parser, and the jail / RSS / entity / breaker ceilings that every other crate depends on for safety. + +**Public interface:** + +`lib.rs` is 47 lines (see `crates/clarion-core/src/lib.rs:1-47`) and is explicit that it is a curated facade per ticket `clarion-29acbcd042`. Re-exports at the crate root, grouped by submodule: + +- **From `entity_id`**: `EntityId`, `EntityIdError`, free function `entity_id(plugin, kind, qualname)` — the cross-language assembler. +- **From `llm_provider`**: trait `LlmProvider`; `OpenRouterProvider` + `OpenRouterProviderConfig`; `RecordingProvider` + `Recording` (test fixture replay); error type `LlmProviderError`; request/response DTOs `LlmRequest` / `LlmResponse` / `LlmPurpose`; `CachingModel`; prompt builders `build_leaf_summary_prompt`, `build_inferred_calls_prompt`, with stable IDs `LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1"` and `INFERRED_CALLS_PROMPT_VERSION = "inferred-calls-v1"`. +- **From `plugin`**: `PluginHost`, `Manifest` + `parse_manifest`, `AcceptedEntity` / `AcceptedEdge` / `AnalyzeFileOutcome` / `AnalyzeFileStats`, `EdgeConfidence`, `UnresolvedCallSite`, `HostError` + `HostFinding`, `JailError`, `CapExceeded`, `DiscoveredPlugin` + `DiscoveryError` + `discover()`, `CrashLoopBreaker` + `CrashLoopState`, and the finding-ID constants (`FINDING_DISABLED_CRASH_LOOP` re-exported at root, with sibling `FINDING_*` constants reachable through `clarion_core::plugin::*`). + +Implementation types deliberately *not* re-exported at the root but still reachable via fully-qualified paths: transport (`Frame`, `read_frame`, `write_frame`, `TransportError`), protocol envelopes (`RequestEnvelope`, `ResponseEnvelope`, `AnalyzeFileParams`, etc.), prlimit helpers, raw entity/edge structs. `make_notification` / `make_request` are `pub(crate)` — `mod.rs:38-42` explains they panic on serde failure and external callers should build envelopes directly. + +**Internal structure:** + +Top-level modules (`crates/clarion-core/src/`): + +- `entity_id.rs` (610 LOC) — `EntityId` newtype + `entity_id()` constructor + `EntityIdError`. Includes the cross-language parity test against `fixtures/entity_id.json` (ADR-003, L2 lock-in). +- `llm_provider.rs` (948 LOC) — single-file LLM abstraction. See breakdown below. +- `plugin/` — supervisor + protocol + safety primitives. Submodule roles documented inline at `plugin/mod.rs:1-12`: + - `manifest.rs` (1508 LOC) — `Manifest`, `PluginMeta`, `Capabilities`, `CapabilitiesRuntime`, `PyrightRuntime`, `Ontology`, `parse_manifest()`, kind-grammar + rule-ID-prefix validators (ADR-021/ADR-022, L5). + - `protocol.rs` (846 LOC) — JSON-RPC 2.0 typed envelopes; `AnalyzeFileParams/Result`, `AnalyzeFileStats`, `UnresolvedCallSite`, `EdgeConfidence`, `InitializeParams/Result`, `Shutdown`, `Exit`, `ProtocolError`. + - `transport.rs` (568 LOC) — `Frame`, `read_frame`/`write_frame`, Content-Length framing with `MAX_HEADER_LINE_BYTES = 8 KiB`; surfaces oversize via `TransportError`. + - `jail.rs` (253 LOC) — `jail()` / `jail_to_string()` canonicalises and asserts containment under project root; `JailError::{EscapedRoot, NonUtf8Path, Io}`. + - `limits.rs` (552 LOC) — `ContentLengthCeiling`, `EntityCountCap`, `PathEscapeBreaker`, `BreakerState`, the finding-ID constants for cap violations, and the Unix `apply_prlimit_as` / `apply_prlimit_nofile_nproc` (no-op stubs on non-Unix). `DEFAULT_MAX_RSS_MIB = 2048` (ADR-021 §2b ceiling). + - `breaker.rs` (360 LOC) — `CrashLoopBreaker`, `CrashLoopState`, `FINDING_DISABLED_CRASH_LOOP` (ADR-002 §UQ-WP2-10). + - `discovery.rs` (637 LOC) — `DiscoveredPlugin`, `DiscoveryError`, `discover()` (Linux only — non-Unix returns empty), `discover_on_path()`, scans `$PATH` for `clarion-plugin-*` executables and pairs them with a sibling `share/clarion/plugins//plugin.toml` (cap 64 KiB). + - `host.rs` (3126 LOC) — see below. + - `mock.rs` (897 LOC, `#[cfg(test)] pub(crate)`) — in-process mock plugin; reachable only from unit tests in this crate. + +### Internal organisation of `plugin/host.rs` (3126 LOC) + +Despite the line count, the file is **not a god-file** — it is structurally one struct (`PluginHost`) with two layers of constructors, an analyse-file pipeline, and a long unit-test suite. Concretely: + +- **Lines 1–155: Module-level constants and finding-ID strings** (`FINDING_*` for entity/edge ontology violations, plus byte caps `MAX_ENTITY_FIELD_BYTES = 4 KiB`, `MAX_ENTITY_EXTRA_BYTES = 64 KiB`, `MAX_UNRESOLVED_CALLEE_EXPR_BYTES = 512`). +- **Lines 157–345: Pure validators / decoders** (`effective_max_nproc`, `oversize_edge_field`, `oversize_field`, `invalid_unresolved_call_site_reason`). +- **Lines 346–438: Public DTOs** — `RawEntity`, `RawEdge`, `RawSource`, `AcceptedEntity`, `AcceptedEdge`, `AnalyzeFileOutcome`, `HostError` (with 17 variants covering Spawn, Handshake, Protocol, EntityCapExceeded, PathEscapeBreakerTripped, OomKilled, Io, etc.). +- **Lines 450–637: `HostFinding` + ~14 named constructors** (`undeclared_kind`, `entity_id_mismatch`, `path_escape`, `disabled_path_escape`, `entity_cap_exceeded_finding`, `unsupported_capability`, `non_utf8_path`, `malformed_entity`, `malformed_edge`, `undeclared_edge_kind`, `edge_field_oversize`, `malformed_unresolved_call_site`, `entity_field_oversize`, `oom_killed`). One constructor per finding type — the "constructor wall" inflates line count but is mechanical. +- **Lines 639–710: `PluginHost` struct definition + `drain_stderr_into_ring`** — generic over reader/writer so subprocess and in-process mock share one impl; `stderr_tail` is a 64 KiB ring buffer. +- **Lines 712–882: Subprocess constructor `PluginHost::spawn`** specialised to `BufReader` / `BufWriter`. This is the heaviest single function — it (1) validates manifest `executable` is a bare basename matching the discovered binary path (anti-redirect defence at host:756–780), (2) applies `RLIMIT_AS` + `nofile` + `nproc` via `pre_exec`, (3) spawns a detached stderr-drain thread, (4) reaps the child on handshake failure (host:864–880 — `Child::Drop` does *not* reap, so failure paths must explicitly wait). +- **Lines 883–957: `PluginHost::connect` + `new_inner` + accessors** (`stderr_tail`, `ontology_version`). +- **Lines 959–1028: `handshake()`** — the four documented steps: send `initialize`, validate response id, run `manifest.validate_for_v0_1()`, send `initialized`. On manifest failure the host is best-effort-shut-down without sending `initialized`. +- **Lines 1031–1198: `analyze_file()`** — the per-file orchestration pipeline. Reads as a numbered validator pipeline: + - `0.` field-size cap → oversize finding, drop (host:1103); + - `1.` ontology declared-kind check (host:1109); + - `2.` entity-id identity check (host:1116); + - `3.` path-jail check + path-escape breaker tick → kill-path on `Tripped` (host:1135); + - `4.` entity-cap check → kill-path on exceed (host:1166). +- **Lines 1200–1299: `process_edges()`** — same drop-on-violation posture, no kill paths (edges don't participate in breakers). +- **Lines 1300–1450: `process_stats`, `shutdown`, `take_findings`, `next_id`, `do_shutdown`, `read_response_matching`** (drain-until-match for stale frames at host:1398; idempotent shutdown via `terminated` flag at host:657). +- **Lines 1452–end (≈1700 LOC of tests)**: 30+ `#[cfg(test)]` named scenarios `t2_…` through `t9_…` plus B.3/B.4*/B.5* regressions. Tests dominate the line count; *production code in `host.rs` is ~1450 LOC*. + +The file is **coherent**: one supervisor type with one validator pipeline. The internal pressure to refactor is mild — splitting findings into a sibling module would shave ~200 LOC, but the drop-on-violation pipeline reads top-to-bottom and benefits from staying co-located. + +### Internal organisation of `llm_provider.rs` (948 LOC) + +Single-file LLM abstraction, organised top-to-bottom (no submodule because there is no `llm_provider/` directory): + +- **Lines 10–11: Stable prompt-ID constants** (`LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1"`, `INFERRED_CALLS_PROMPT_VERSION = "inferred-calls-v1"`). These form two of the five components of the ADR-007 cache key; the other three (`entity_id`, `content_hash`, `model_tier`, `guidance_fingerprint`) are assembled in `clarion-storage::cache::SummaryCacheKey`. **The 5-tuple is *not* materialised inside this file** — the provider is dispatch-only; cache keying happens in `clarion-storage` and `clarion-mcp`. +- **Lines 13–37: Request / response / purpose DTOs** (`LlmRequest`, `LlmResponse`, `LlmPurpose::{Summary, InferredEdges}`). +- **Lines 38–82: Error taxonomy** — `LlmProviderError` with six variants; `retryable()` returns the inner retryable flag for `Http`/`Provider`/`InvalidResponse`, false for `MissingRecording`/`LiveProviderNotAllowed`/`MissingApiKey`. +- **Lines 84–90: The `LlmProvider` trait** — five required methods: `name`, `invoke`, `estimate_tokens`, `tier_to_model`, `caching_model`. Trait is `Send + Sync` so providers can be shared across MCP request handlers behind an `Arc`. +- **Lines 92–151: `RecordingProvider`** — test-mode provider that replays exact-shape `LlmRequest` matches from a fixed `Vec`. Tracks invocations in a `Mutex>` for assertion. Returns `MissingRecording` (non-retryable) on shape drift. +- **Lines 153–295: `OpenRouterProvider`** — the live provider. + - Config gate at `from_config` (lines 173–187): requires both `allow_live_provider == true` AND a non-empty `api_key`; either failure yields `LiveProviderNotAllowed` / `MissingApiKey` (both non-retryable). + - `invoke()` (lines 202–279): blocking `reqwest` POST to `{endpoint}/chat/completions`, 60s timeout, `Authorization: Bearer`, `HTTP-Referer`, `X-OpenRouter-Title` headers. Payload includes `"temperature": 0`, `"provider": {"require_parameters": true}`, and `response_format` from `response_format_for_purpose()`. + - **The strict-JSON path** (the open question from §8) lives at `response_format_for_purpose` (lines 297–370): two JSON-Schema objects, both with `"strict": true` and `"additionalProperties": false`. `Summary` enforces `{purpose, behavior, relationships, risks}`; `InferredEdges` enforces `edges: [{site_key, target_id, confidence, rationale}]`. This is the B.8 GREEN-rerun fix from commit `ab6b1dd` — without `"strict": true` OpenRouter providers silently produced free-form text. + - Error unwrap chain: the response body is first parsed as `OpenRouterErrorEnvelope` (line 250) — even on HTTP 200, choices can carry per-call provider errors at `OpenRouterChatResponse::output_text` (line 379), which surfaces `LlmProviderError::Provider`. +- **Lines 297–500: HTTP plumbing** — response struct definitions (`OpenRouterChatResponse`, `OpenRouterChoice`, `OpenRouterMessage`, `OpenRouterUsage`, `OpenRouterErrorEnvelope`, `OpenRouterErrorBody`), `provider_error_from_body`, `retryable_status` (true for 408 / 429 / ≥500), `retry_after_seconds` (header parse), `estimate_text_tokens` (chars/4 heuristic). +- **Lines 502–561: Prompt builders** — `LeafSummaryPromptInput` / `InferredCallsPromptInput` DTOs and the two `build_*_prompt` functions emitting `PromptTemplate { id, body }`. Body is a hand-written `format!` template; no Tera/Handlebars. +- **Lines 563–end: Unit tests**, including a TCP-listener-based in-process OpenRouter stub at `openrouter_provider_invokes_chat_completions_and_extracts_usage_tokens`. + +**Nothing is cached inside `llm_provider.rs`.** The provider is a stateless dispatcher; caching is `clarion-storage::cache` (per discovery §4, Subsystem B) and lookup is performed by callers in `clarion-mcp::lib.rs` and the analyze-file inferred-edges path. Caching is *lazy and lookup-driven*: callers compute `SummaryCacheKey` from the 5-tuple, hit the cache, and only call `LlmProvider::invoke` on miss — then write the response back keyed on the same tuple. + +**Key types & traits:** + +| Type | Where | Why callers touch it | +|---|---|---| +| `EntityId`, `entity_id()` | `entity_id.rs` | Every accepted entity is identified by this; cross-language parity proof. | +| `LlmProvider` (trait) | `llm_provider.rs:84` | MCP and analyze layers receive `Arc` for dispatch. | +| `OpenRouterProvider`, `RecordingProvider` | `llm_provider.rs:164`, `:99` | Provider construction in `clarion-cli::serve.rs`. | +| `PluginHost` | `host.rs:639` | The per-file supervisor; `spawn` for production, `connect` for in-process tests. | +| `AcceptedEntity`, `AcceptedEdge`, `AnalyzeFileOutcome` | `host.rs:346–398` | Hand-off shapes from host → analyse orchestrator → writer-actor. | +| `Manifest` + `parse_manifest` | `manifest.rs:115`, `:281` | `clarion-cli::analyze` reads `plugin.toml` through this; `PluginHost` consumes it. | +| `CrashLoopBreaker` | `breaker.rs:43` | `clarion-cli::analyze` ticks this per plugin-spawn failure. | +| `discover()` / `DiscoveredPlugin` | `discovery.rs:133`, `:47` | Plugin discovery on `$PATH`. | +| `HostError` / `HostFinding` | `host.rs:400`, `:450` | Error matching + finding emission for operator diagnostics + Filigree forwarding. | +| `LlmProviderError` | `llm_provider.rs:44` | Caller uses `.retryable()` to drive WP6 backoff. | + +**Dependencies (workspace + outbound):** + +- **Inbound** (per `grep clarion-core` against each Cargo.toml): + - `clarion-storage/Cargo.toml:13` + - `clarion-mcp/Cargo.toml:13` + - `clarion-cli/Cargo.toml:20` + + *Note (corrected by validation pass):* `clarion-plugin-fixture` **does** depend on `clarion-core` for the typed protocol structs only (`use clarion_core::plugin::*` in its `main.rs`; declared at `crates/clarion-plugin-fixture/Cargo.toml:18` as `clarion-core = { path = "../clarion-core", version = "0.1.0-dev" }`). It does not link against the supervisor / writer / MCP paths. The fixture is consumed only via subprocess in `wp2_e2e`. + +- **Outbound** (`Cargo.toml`): + - `reqwest` (workspace: `rustls-tls-native-roots`, blocking + JSON) — only `llm_provider.rs`. + - `serde` + `serde_json` + `toml` — DTO + manifest parsing. + - `thiserror` — every error enum here. + - `tracing` — host stderr-drain failures + best-effort-shutdown diagnostics. + - `nix` (workspace, `resource` feature only) — `apply_prlimit_*` in `limits.rs`. The single `unsafe` allowance in the workspace lives here (`pre_exec` + `setrlimit`); workspace lint floor is `unsafe_code = "deny"` (downgraded from `forbid` per documented exception in workspace `Cargo.toml`). + - `tempfile` (dev-dep) — tests only. + +- **Notably absent**: no `tokio` dependency. The plugin host is fully synchronous (`BufRead + Write` generic bounds, blocking `reqwest`). Async is introduced one layer up in `clarion-storage::writer` (`tokio::task`) and `clarion-mcp::lib.rs`. + +**Patterns observed:** + +- **Generic reader/writer typestate-lite** — `PluginHost` is generic; `spawn` returns a host parameterised on `BufReader` / `BufWriter`, while `connect` accepts any `BufRead + Write` pair so the in-process `mock.rs` and the e2e tests share one validator pipeline. +- **Drop-on-violation pipeline with discrete kill-paths** — `analyze_file` is a numbered five-step validator; steps 0–2 only emit findings and drop the offending record; steps 3–4 escalate to plugin termination if a breaker trips. The kill-paths route through a single `do_shutdown` (host:1352) that handles the idempotent-shutdown flag. +- **Newtype-with-constructor for safety-critical IDs** — `EntityId(String)` is private-field; the only constructors live in `entity_id.rs` and validate the grammar before producing the newtype. `FromStr` rebuilds via the same constructor. +- **Trait-object provider dispatch** — `Arc` consumed by MCP and analyze; live vs recording vs disabled selected at config time (`clarion-cli::serve.rs`). +- **Finding-ID constants as first-class API** — every `FINDING_*` is a `pub const &str` exported at module root so callers (and tests) can `assert_eq!` on the stable ID rather than match on free-form messages. The ID grammar (`CLA-INFRA-*`) is asserted at manifest-parse time (`manifest.rs:414`). +- **Pure-function validators** — `oversize_field`, `oversize_edge_field`, `invalid_unresolved_call_site_reason`, `validate_kind_string`, `validate_rule_id_prefix_grammar` are all stateless and unit-tested in isolation. + +**Concerns / risks:** + +- **`host.rs` size** (3126 LOC including ~1700 LOC of tests). Production code is ~1450 LOC and is coherent, but the file is the codebase's largest. A future refactor could move the 14 `HostFinding` constructors and the `FINDING_*` constants to a sibling `host_findings.rs` for ~200 LOC saved without altering semantics. +- **`manifest.rs` size** (1508 LOC) — not deep-read in this pass; the public type surface is small (one `Manifest` + five field-structs + one error enum + parser + two grammar validators). Likely test-dominated like `host.rs`, but worth a separate confirm pass. +- **Subprocess constructor is Linux-coupled** — `spawn` at `host.rs:739` uses `pre_exec` + `RLIMIT_AS`/`RLIMIT_NOFILE`/`RLIMIT_NPROC`. `limits.rs:330–342` provides no-op stubs for non-Unix targets, but `discover()` at `discovery.rs:139` is also `#[cfg(unix)]` and returns empty on Windows. v0.1 is Linux-only by intent (per Sprint-1 sign-off), but the cross-platform doors are stubs, not implementations. +- **Reqwest blocking inside a `Send + Sync` trait method** — `LlmProvider::invoke` is sync. Callers from async contexts (`clarion-mcp`) must `spawn_blocking`. Not verified in this pass which side actually does the offloading; if callers run `invoke` on the runtime thread, MCP tool handlers can starve. This belongs as a follow-up question for the `clarion-mcp` catalog pass. +- **OpenRouter strict-JSON regression risk** — the `"strict": true` JSON-Schema gates were added in commit `ab6b1dd` for B.8 GREEN; the path lives entirely in `response_format_for_purpose` (`llm_provider.rs:297`) and is asserted by a test that pattern-matches the serialised request body. A schema change anywhere in the prompt-output contract must update both the prompt template (`build_*_prompt`) and the strict-JSON schema in lockstep — there is no cross-check between them. +- **`unsafe` allowance lives here** — `pre_exec` + `setrlimit` is the workspace's sole `unsafe` block (documented in workspace `Cargo.toml`). Any new unsafe in `clarion-core` should require an ADR amendment. +- **No `tokio` use, but exported types flow into async runtimes** — `AcceptedEntity` / `AcceptedEdge` cross the async boundary via `clarion-storage::WriterCmd`. The DTOs are `Clone + Send` (verified through usage patterns) but this is not enforced by trait bounds at the public boundary; a future field that is not `Send` would silently break downstream. +- **Test-only `mock.rs` (897 LOC) lives inside `src/` under `#[cfg(test)]`** rather than in `tests/`. Pro: integration tests in `tests/wp2_e2e.rs` cannot link against it — keeping mock scaffolding off the public surface is exactly the goal (`mock.rs` is `pub(crate)`). Con: 897 LOC of test scaffolding inflates `clarion-core` source counts; deferred items include `clarion-adeff0916d` (fixture-binary self-build) which may consolidate this. + +**Confidence:** High — read `lib.rs` and `plugin/mod.rs` in full; read `host.rs` structural skeleton + `PluginHost` definition + `spawn` constructor + full `analyze_file` body; read `llm_provider.rs` in full through line 561 (the production code; tests sampled); cross-verified inbound deps via `grep clarion-core` against each crate's `Cargo.toml`. Two claims are Medium-confidence and called out above: (a) `manifest.rs` internal proportions not directly verified beyond signature scan; (b) whether MCP wraps `LlmProvider::invoke` in `spawn_blocking` is out-of-scope for this pass and listed as a follow-up. +## clarion-storage + +**Location:** `crates/clarion-storage/` + +**Responsibility:** Persists Clarion's entity/edge graph, run provenance, and LLM caches in a single SQLite database under `.clarion/clarion.db`. All mutations funnel through a single writer-actor task (sole `rusqlite::Connection`); all reads come from a `deadpool-sqlite` pool. The crate also owns the schema migration runner, the PRAGMA discipline, the edge-contract validator, and the typed query helpers consumed by `clarion-mcp` and `clarion-cli`. + +### Internal structure + +**Module roster** (`src/lib.rs:7–15`, all `pub mod`): + +| Module | LOC | Role | +|---|---|---| +| `writer.rs` | 817 | Writer-actor: spawn, command loop, edge-contract enforcement, per-N batch commits, parent/contains consistency check at `CommitRun` | +| `query.rs` | 569 | Read-side helpers (graph navigation, FTS-or-LIKE search, unresolved call-site fan-out) | +| `cache.rs` | 251 | `SummaryCacheKey` (5-tuple per ADR-007) + `InferredEdgeCacheKey` (4-tuple) and their upsert/lookup/touch helpers | +| `commands.rs` | 183 | `WriterCmd` enum (9 variants) + POD records + `RunStatus` | +| `schema.rs` | 118 | Embed-and-apply migration runner (`include_str!` of the single `.sql` file) | +| `reader.rs` | 88 | `ReaderPool` wrapper around `deadpool-sqlite::Pool` | +| `unresolved.rs` | 50 | Replace-by-caller bookkeeping for unresolved call sites | +| `error.rs` | 48 | `StorageError` taxonomy (11 variants, `thiserror`) | +| `pragma.rs` | 45 | WAL/synchronous=NORMAL/busy_timeout=5000/foreign_keys=ON discipline | +| `lib.rs` | 35 | Curated `pub use` facade | + +**Schema (ER summary)** — single migration `migrations/0001_initial_schema.sql` (289 LOC). Eight base tables, one FTS5 virtual table, three triggers, one view, two generated columns: + +``` + ┌─────────────────────────────────────────────┐ + │ entities (PK id TEXT) │ + │ + virtual cols scope_level / scope_rank │ + │ + indexes on kind, plugin_id, parent_id, │ + │ source_file_id, source_file_path, │ + │ content_hash, last_seen_commit, │ + │ scope_rank (partial), git_churn (partial)│ + └──┬──────────────────┬────────┬─────────────┘ + │self-ref │FK FK │FK + parent_id │ source_file_id │ │ + ▼ ▼ ▼ + ┌──────────────┐ ┌──────────────────────────────────────┐ + │ entity_tags │ │ edges WITHOUT ROWID │ + │ (entity_id, │ │ PK (kind, from_id, to_id) │ + │ tag) PK │ │ CHECK confidence IN │ + │ ON DELETE │ │ (resolved, ambiguous, inferred) │ + │ CASCADE │ │ FKs: from_id, to_id, source_file_id │ + └──────────────┘ │ ALL ON DELETE CASCADE │ + └──────────────────────────────────────┘ + ▲ ▲ + │entity_id FK │caller_entity_id FK + ┌─────────────────────┐ ┌────────────────────────────────┐ + │ findings (PK id) │ │ entity_unresolved_call_sites │ + │ CHECK kind ∈ 5 │ │ PK (caller_entity_id, │ + │ CHECK severity ∈ 5 │ │ caller_content_hash, │ + │ CHECK status ∈ 4 │ │ site_key) │ + │ FK entity_id │ └────────────────────────────────┘ + └─────────────────────┘ + ▲caller_entity_id FK + ┌────────────────────────────┐ ┌──────────────────────────┐ + │ inferred_edge_cache │ │ summary_cache │ + │ PK (caller_entity_id, │ │ PK 5-tuple (entity_id, │ + │ caller_content_hash, │ │ content_hash, │ + │ model_id, │ │ prompt_template_id, │ + │ prompt_version) │ │ model_tier, │ + │ FK caller_entity_id │ │ guidance_fingerprint)│ + └────────────────────────────┘ │ CHECK stale_semantic∈(0,1)│ + └──────────────────────────┘ + + ┌──────────────────────────┐ ┌────────────────────────────┐ + │ runs (PK id) │ │ schema_migrations │ + │ CHECK status ∈ (running, │ │ (version PK, name, │ + │ skipped_no_plugins, │ │ applied_at) │ + │ completed, failed) │ └────────────────────────────┘ + └──────────────────────────┘ + + FTS5 virtual: entity_fts (entity_id UNINDEXED, name, short_name, + summary_text, content_text); kept in sync by triggers + entities_ai / entities_au / entities_ad. + + View: guidance_sheets — projects entities WHERE kind='guidance' + with json_extract of `properties` + json_group_array of tags. +``` + +ADR-031 `CHECK` discipline (lines 89, 107–112, 124–125, 153, 200–201): closed core-owned vocabularies receive `CHECK` clauses (`edges.confidence`, `findings.{kind, severity, status}`, `summary_cache.stale_semantic`, `runs.status`). Plugin-extensible vocabularies deliberately omit `CHECK` per ADR-022 — `entities.kind` (`migrations/0001_initial_schema.sql:33–36`) and `edges.kind` (`migrations/0001_initial_schema.sql:77–81`); enforcement at those columns is the writer-actor (`writer.rs::enforce_edge_contract` for edges, manifest acceptance for entity kinds). + +**Writer-actor command set** (`commands.rs::WriterCmd`, 9 variants): + +| Variant | Lifecycle | Notes | +|---|---|---| +| `BeginRun` | analyze-time | `runs` INSERT with `status='running'`, opens `BEGIN` (`writer.rs:308–330`) | +| `InsertEntity` | analyze-time | Single INSERT into `entities`; counts toward batch boundary (`writer.rs:332–390`) | +| `InsertEdge` | analyze-time | Calls `enforce_edge_contract` (`writer.rs:411–472`) then `INSERT OR IGNORE`; dedupe increments `dropped_edges_total`, ambiguous accepts bump `ambiguous_edges_total` (`writer.rs:474–520`) | +| `InsertInferredEdges` | query-time (MCP) | Upserts inferred-edge cache row, GCs stale inferred edges for the caller, inserts new ones; refuses to shadow static resolved/ambiguous calls (`writer.rs:522–599`) | +| `UpsertSummaryCache` | query-time (MCP) | 5-tuple upsert on `summary_cache` (`cache.rs:48–85`) | +| `TouchSummaryCache` | query-time (MCP) | `UPDATE summary_cache SET last_accessed_at` (`cache.rs:112–132`) | +| `ReplaceUnresolvedCallSitesForCaller` | analyze-time | Delete-then-insert pattern; replaces all sites for one caller atomically inside the run transaction (`writer.rs:601–621`, `unresolved.rs:20–50`) | +| `CommitRun` | analyze-time | Runs the B.3 parent/contains dual-encoding check **inside** the open transaction (`writer.rs:733–796`); on mismatch rolls back the run's writes and marks `runs.status='failed'` with `CLA-INFRA-PARENT-CONTAINS-MISMATCH` in `stats.failure_reason`; on success folds the `runs` UPDATE into the final COMMIT (`writer.rs:671–727`) | +| `FailRun` | analyze-time | ROLLBACK + `UPDATE runs SET status='failed'` (`writer.rs:798–817`) | + +The actor multiplexes analyze-time and query-time mutations on the same connection. `query_time_write` (`writer.rs:647–669`) commits any open analyze-time batch, runs the MCP write, and reopens a `BEGIN` if a run is still active — so analyze-time and MCP traffic cannot deadlock or interleave on the same transaction. Batch cadence is `DEFAULT_BATCH_SIZE = 50` writes (`writer.rs:35`, `bump_writes_and_maybe_commit` at `writer.rs:628–645`); the `INSERT OR IGNORE` edge dedupe is workload-shape-invariant because UNIQUE conflicts still bump the batch counter. + +Channel-closed cleanup (`writer.rs:251–273`): if the `Writer` is dropped mid-run, the actor self-heals by issuing `ROLLBACK` and marking the surviving run row `failed` with `failure_reason="writer channel closed unexpectedly"`. This is the durability backstop for the supervisor in `clarion-cli::analyze`. + +**Edge contract** (`writer.rs::enforce_edge_contract`, line 411). Ontology is hard-coded as `STRUCTURAL_EDGE_KINDS = ["contains", "in_subsystem", "guides", "emits_finding"]` (`writer.rs:394`) and `ANCHORED_EDGE_KINDS = ["calls", "references", "imports", "decorates", "inherits_from"]` (`writer.rs:395–401`) — nine kinds total per ADR-026/028. Structural edges MUST have `confidence=resolved` and NULL `source_byte_*`; anchored edges MUST have both `source_byte_*` set, and may NOT be `inferred` at scan time (`writer.rs:440–449`) because inferred-tier edges are query-time-only. Violations return `StorageError::WriterProtocol` with one of three CLA codes (`CLA-INFRA-EDGE-CONFIDENCE-CONTRACT`, `CLA-INFRA-EDGE-SOURCE-RANGE-CONTRACT`, `CLA-INFRA-EDGE-UNKNOWN-KIND`) so the surrounding `runs.stats.failure_reason` carries the code (`writer.rs:402–410`). + +**Reader pool** (`reader.rs`). `ReaderPool::open` builds a `deadpool_sqlite::Pool` with `Runtime::Tokio1` and a caller-supplied `max_size` (the CLI passes its own value; tests use small caps). `with_reader` acquires from the pool, submits a `'static` closure to deadpool's `interact()` blocking task pool, and applies read-side PRAGMAs (`busy_timeout=5000`, `foreign_keys=ON`) on every acquisition. Retry-on-`SQLITE_BUSY` is delegated to SQLite itself via `busy_timeout` rather than an application-level loop — both writer and readers wait up to 5 s for the lock. WAL mode (set on the writer's first connection, `pragma.rs:16–31`) is what lets readers proceed concurrently without seeing in-flight writes. `waiting_count()` (`reader.rs:85–87`) is exposed `#[doc(hidden)]` for deterministic test polling. + +**Cache keys.** `SummaryCacheKey` (`cache.rs:7–14`) materialises ADR-007's 5-tuple exactly: `(entity_id, content_hash, prompt_template_id, model_tier, guidance_fingerprint)`. `ontology_version` is *not* in the key (correct per ADR-007 — that field is handshake validation only). `InferredEdgeCacheKey` (`cache.rs:30–36`) is a 4-tuple `(caller_entity_id, caller_content_hash, model_id, prompt_version)`. **Boundary clarification**: cache lookup/upsert helpers in `cache.rs` are pure storage operations; on a miss, `clarion-mcp::lib.rs` decides whether to call the LLM (via `clarion-core::LlmProvider`), then enqueues the result via `WriterCmd::UpsertSummaryCache` or `WriterCmd::InsertInferredEdges`. This crate does not depend on `clarion-core::LlmProvider`; its only `clarion-core` dependency is `EdgeConfidence` (`commands.rs:14`, `query.rs:6`). + +**Query helpers re-exported via `lib.rs`** (`lib.rs:27–32`): `entity_by_id`, `entity_at_line` (innermost-entity-at-line with tie-break by source-range size then kind preference function→class→module), `find_entities` (FTS5 if the pattern is alnum/underscore; LIKE-with-escape otherwise — see `is_fts_safe` at `query.rs:552`), `call_edges_from` / `call_edges_targeting` (apply ADR-028 confidence ceiling; for `ambiguous` edges, expand the `properties.candidates[]` JSON array into multiple match rows — `query.rs:218–235`, `523–534`), `contained_entity_ids` (iterative DFS over `contains` edges with cycle guard and `max_entities` truncation — `query.rs:354–388`), `unresolved_call_sites_for_caller`, `unresolved_callers_for_target` (LIKE-suffix match on `callee_expr` with same-file preference — `query.rs:294–332`), `candidate_entities_for_unresolved_sites`, `child_entity_ids`, `normalize_source_path` (project-root jail; both lexical normalisation and `canonicalize()` are checked — `query.rs:76–104`). + +### External interface + +`lib.rs` (35 LOC) re-exports a closed surface: the `WriterCmd`/`EdgeRecord`/`EntityRecord`/`RunStatus` typed boundary; `Writer` and the two channel/batch constants; `ReaderPool`; the query helpers; the cache key types and their three pure helpers (`summary_cache_lookup`, `inferred_edge_cache_lookup`, `inferred_edge_cache_key_id`); `StorageError`/`Result`. Internal modules `pragma` and `schema` are `pub mod`, used by `clarion-cli::install` (`crates/clarion-cli/src/install.rs:20`). `clarion-mcp::lib.rs:22–30` consumes 18 named symbols; `clarion-cli::analyze.rs:24–27` consumes 4 (writer/command shapes only). + +### Dependencies + +- **Inbound** (verified via `use clarion_storage::` grep): + - `clarion-mcp` — full read surface + the four query-time `WriterCmd` variants + - `clarion-cli` — `analyze.rs` (writer + commands), `install.rs` (`pragma` + `schema`), `serve.rs` (`Writer` + `ReaderPool` + batch constants) +- **Outbound** (`Cargo.toml`): + - `clarion-core` — only for `EdgeConfidence` (used in `commands.rs` + `query.rs`); intentionally minimal + - `deadpool-sqlite 0.8` — async-friendly read pool (ADR-011) + - `rusqlite 0.31` — bundled SQLite, sole write driver + - `tokio` — `mpsc` + `oneshot` channels, `spawn_blocking` for the writer task + - `serde_json` — JSON shape validation on `InferredCallEdgeRecord.properties_json` + `ambiguous` `candidates[]` decoding + - `thiserror`, `tracing` + +No outbound dependency on `clarion-mcp`, `clarion-cli`, or any plugin crate. Crate-level acyclicity holds. + +### Patterns observed + +- **Actor + pool split (ADR-011).** Single writer task owns the write connection; all multi-row mutations are batched into a transaction sized by writes (entity inserts + edge insert attempts, including dedupes). The pattern is documented as L3 lock-in (`writer.rs:1–13`). +- **Typed command boundary.** Every mutation is a `WriterCmd` variant carrying its own `oneshot::Sender>` ack — per-command response, no batched fan-in. Adding a new mutation is a single-file append (`commands.rs`) plus a match arm (`writer.rs:152–249`). +- **Defence in depth on closed vocabularies (ADR-031).** Two enforcement layers: the writer-actor (canonical) and SQL `CHECK` (backstop). The migration's per-column comments name which ADR closes each vocabulary; plugin-extensible columns are explicitly tagged "no CHECK by policy." +- **Edge-contract failure codes are findings.** When `enforce_edge_contract` rejects, the error message embeds `CLA-INFRA-EDGE-*` codes that surface in `runs.stats.failure_reason` — making writer-rejected edges observable as machine-greppable findings rather than opaque protocol errors. +- **`query_time_write` interleaves cleanly.** Query-time MCP writes commit the analyze-batch first, then reopen `BEGIN` if a run is still in progress — the actor never holds an MCP cache row open inside an analyze transaction. +- **Validation depth on path inputs.** `normalize_source_path` does lexical normalisation *and* `canonicalize()`, and checks containment against the canonicalized project root in both forms (`query.rs:76–104`). Prevents symlink/`..` escape against `entity_at_line` and `find_entity`. +- **B.3 dual-encoding check at commit.** Parent/contains consistency is verified inside the transaction at `CommitRun` time (`writer.rs:733–796`), so an inconsistent run rolls back rather than persisting a half-corrupt graph. + +### Concerns + +- **Single migration, edit-in-place under ADR-024.** `migrations/0001_initial_schema.sql` has been edited three times (initial; 2026-05-03 ADR-024 vocabulary rename; 2026-05-18 ADR-031 `CHECK` clauses). The retirement trigger is documented in-file (`0001_initial_schema.sql:10–16`) but no automated check fires when the trigger condition (external operator builds `.clarion/clarion.db` from a published Clarion build) is met. Manual discipline only. Mitigated by the migration's own `schema_migrations` row idempotence (`schema.rs:81–89`). +- **Edge ontology is duplicated.** `STRUCTURAL_EDGE_KINDS` + `ANCHORED_EDGE_KINDS` are hard-coded in `writer.rs:394–401`; ADR-026/028 are the design source; the Python plugin's manifest declares `edge_kinds = ["contains", "calls", "references"]` independently. A new kind requires edits in at least three places (manifest, writer, ADR). No compile-time enforcement that these stay in sync. +- **Schema-shape FK in `entities.source_file_id` is self-referential** (`migrations/0001_initial_schema.sql:40`). Works because source-file entities are inserted before their contained functions/classes (plugin traversal order), but there is no constraint that enforces insertion order. A plugin emitting children before parents would fail with an FK violation, surfacing as an opaque `rusqlite::Error` rather than a writer-protocol error. +- **`busy_timeout=5000` is the only `SQLITE_BUSY` mitigation.** Under heavy contention a reader can fail with a SQLite-level busy error rather than being retried at the application layer. The B.8 scale test exercises this path in practice; no per-attempt retry loop exists in `with_reader`. +- **`InsertEdge` and `InsertEntity` share a single batch counter.** An edge-heavy file (e.g., a module with many `references` edges) can flush the batch boundary mid-file. Documented behaviour (`writer.rs:285–289`) but worth flagging — long transactions are not bounded by file boundary. +- **No write-side throttling on `WriterCmd` channel.** `DEFAULT_CHANNEL_CAPACITY = 256` (`writer.rs:38`); a faster producer than the actor will block via `Sender::send().await` backpressure, which is correct, but no metric is exposed for "time spent blocked on writer queue." + +### Confidence + +**Confidence:** High — Read 100% of every `src/*.rs` module (10 files, 1 950 LOC) and the migration in full (289 LOC). Cross-validated dependency direction by grepping `use clarion_storage::` across the workspace: only `clarion-mcp` and `clarion-cli` consume it; no inbound cycles. Confirmed `WriterCmd` variant count (9) matches the actor's match arms one-to-one. Schema CHECK constraints verified at exact line numbers against ADR-031's "closed vs. extensible" decision. Edge-contract code-paths (`enforce_edge_contract` and the three CLA codes it emits) read end-to-end. ADR cross-references are inline in both the migration and the writer source, so the "ADR says X / code does Y" gap is small. +## clarion-mcp + +**Location:** `crates/clarion-mcp/` + +**Responsibility:** Speaks MCP protocol revision `2025-11-25` over stdio; serves seven storage-backed read tools (`entity_at`, `find_entity`, `callers_of`, `execution_paths_from`, `summary`, `issues_for`, `neighborhood`) to consult-mode LLM agents, with on-demand LLM dispatch for leaf-scope summaries and inferred call edges, and optional Filigree enrichment for issue attachment. + +**Key Components:** + +- `src/lib.rs` (2620 LOC) — single-file crate root. Internal organisation, top-to-bottom: + - **Protocol surface** (lines 36–166): `MCP_PROTOCOL_VERSION = "2025-11-25"` constant (line 36), `ToolDefinition` struct (40–45), `list_tools()` returning seven hardcoded `ToolDefinition`s with inline JSON-Schema (48–120), schema helpers `confidence_schema` / `id_schema` / `id_confidence_schema` (122–151), stateless `handle_json_rpc` router (154–166) wired to `initialize` / `tools/list` / `tools/call`. + - **`ServerState`** (168–1252): the central handler. Fields (168–178): `project_root: PathBuf`, `readers: ReaderPool`, `execution_edge_cap: usize` (default 500), `summary_llm: Option`, `clock: Arc String + Send + Sync>`, `budget: Arc>`, `inferred_inflight: Arc>>>` (in-flight dispatch coalescing), `filigree_client: Option>`. Builder methods (180–226): `new`, `with_edge_cap`, `with_summary_llm`, `with_clock`, `with_filigree_client`. + - **Per-tool dispatch** (228–294): instance `handle_json_rpc` + `handle_tool_call` route by name to seven `tool_*` async methods. + - **Per-tool handlers** (296–717): `tool_entity_at` (296–319), `tool_find_entity` (321–354), `tool_callers_of` (356–391), `tool_execution_paths_from` (393–434) + `inferred_execution_paths` (436–520), `tool_neighborhood` (522–581), `tool_issues_for` (583–671), `tool_summary` (673–717). + - **LLM inferred-edges pipeline** (719–995): `ensure_inferred_for_target` / `ensure_inferred_for_caller` (719–796) — entry points called by `callers_of`/`neighborhood`/`execution_paths_from` when `confidence == Inferred`; `read_inferred_inputs` (798–833) builds an `InferredEdgeCacheKey` from caller content-hash + model_id + prompt_version (ADR-007); `materialize_cached_inferred` (835–863) on cache hit; `coalesced_inferred_dispatch` (865–908) deduplicates concurrent dispatches via a `broadcast` channel with a 60-second timeout; `perform_inferred_dispatch` (910–995) builds the prompt via `clarion_core::build_inferred_calls_prompt`, reserves budget, invokes the provider on a `spawn_blocking` task, then sends `WriterCmd::InsertInferredEdges` to the writer-actor. + - **LLM summary pipeline** (997–1155): `read_summary_inputs` (997–1035) keys against `SummaryCacheKey { entity_id, content_hash, prompt_template_id = LEAF_SUMMARY_PROMPT_TEMPLATE_ID, model_tier, guidance_fingerprint = "guidance-empty" }` — five-tuple cache key matching ADR-007; `cached_summary_envelope` (1037–1060) bumps `last_accessed_at` via `WriterCmd::TouchSummaryCache`; `refresh_summary` (1062–1155) on miss invokes provider, then `WriterCmd::UpsertSummaryCache`. ADR-030 leaf-scope is encoded by the single `LEAF_SUMMARY_PROMPT_TEMPLATE_ID` template and the `summary` tool description (line 98). + - **Writer-actor helper + budget** (1157–1251): `send_writer` (1157–1171) — oneshot ack roundtrip pattern; `BudgetLedger` accounting with `reserve_budget` / `BudgetReservation::commit` / `Drop` rollback (1180–1316); `summary_model_id` / `inferred_edges_model_id` / `max_inferred_edges_per_caller` (1221–1251) honour `LlmProvider::tier_to_model("summary"|"inferred_edges")`. + - **Plain types** (1266–1607): `SummaryLlmState`, `BudgetLedger`, `SummaryRead` enum, `SummaryReady`, `IssuesForRead`, `IssuesForAccumulator` (drift-classifier matching `content_hash_at_attach` against current `entities.content_hash`, lines 1379–1411, with 100-issue cap), `InferenceLlmState`, `InferredRead`, `InferredDispatchStats` (aggregated stats_delta), `InferredDispatchFailure`, `InferredDispatchOutcome`, `InferredCallsResponse` / `InferredCallsResponseEdge`. + - **Transport loop** (1609–1686): `McpError` enum, `handle_frame` / `handle_frame_with_state`, `serve_stdio` / `serve_stdio_with_state` / `serve_stdio_with_state_on_runtime` — Content-Length frame loop using `clarion_core::plugin::{read_frame, write_frame, ContentLengthCeiling::DEFAULT, Frame, TransportError}`; treats `UnexpectedEof` as clean shutdown. + - **Stateless `handle_tool_call`** (1701–1736): a stub kept for the stateless `handle_json_rpc` router; emits `tool-unimplemented` envelopes for every tool — only reachable from the stateless entry point used by tests and `handle_frame`. + - **Envelope/parsing helpers** (1738–2419): `ParamError`, `PathTraversal` (recursive walker for `execution_paths_from`, 1755–1802), `ReferenceDirection`, `required_str` / `required_i64` / `optional_usize` / `optional_bool` / `optional_confidence` argument coercers, envelope builders (`success_envelope`, `tool_error_envelope`, `tool_error_envelope_with_diagnostics`, `success_envelope_with_truncation_and_stats`), `entity_json`, `source_excerpt` + `line_range_excerpt` + `truncate_excerpt`, `inferred_records_from_result` (parses LLM JSON into `InferredCallEdgeRecord`, 2216–2266), `summary_cache_expired` + `timestamp_day_index` + `days_from_civil` (Howard Hinnant civil-from-days algorithm for the 180-day TTL), `caller_json` / `callee_json` / `path_json` / `reference_neighbors`. + - **Unit tests** (2421–2620): 8 tests covering tool-list exact docstrings, initialize result, tools/list wrapping, unknown method/tool/params, frame dispatch round-trip, and multi-frame serve-stdio. +- `src/config.rs` (352 LOC) — `McpConfig` (YAML via `serde_norway`) with `llm` and `integrations.filigree` sections; `LlmConfig` (provider, `enabled`, `allow_live_provider`, `session_token_ceiling: u64` default 1_000_000, `model_id` default `"anthropic/claude-sonnet-4.6"`, `cache_max_age_days` default 180, `max_inferred_edges_per_caller` default 8); `LlmProviderKind::{OpenRouter, Anthropic, Recording}` (with Anthropic actively rejected — `ConfigError::DeprecatedProvider` with code `CLA-CONFIG-DEPRECATED-PROVIDER`, lines 34–43, 169–171); accepts `llm_policy` alias for the `llm` block (line 10, test at 270–284); `select_provider_with_env` (156–191) returns `ProviderSelection::{Disabled, Recording, OpenRouter{api_key_env}}` — opt-in to live OpenRouter is gated by `allow_live_provider` *or* the `CLARION_LLM_LIVE=1` env (173); presence of an API key alone is not enough (test at 287–303); `FiligreeConfig` (127–147) — `enabled` default false, `base_url` default `http://127.0.0.1:8766`, `actor` default `clarion-mcp`, `token_env` default `FILIGREE_API_TOKEN`, `timeout_seconds` default 5. Five unit tests. +- `src/filigree.rs` (238 LOC) — `EntityAssociationsResponse` / `EntityAssociation` (Filigree ADR-029 contract); `FiligreeLookup` trait (45–50); `FiligreeHttpClient` (52–111) — blocking `reqwest::blocking::Client` with `timeout_seconds.max(1)`, returns `Ok(None)` when `enabled=false` (68–70); `associations_for` GETs `{base_url}/api/entity-associations?entity_id={encoded}` with `x-filigree-actor` and optional `Bearer` token; manual percent-encoding restricted to unreserved chars (127–142); three unit tests including a real TCP-server roundtrip (194–237). +- `tests/storage_tools.rs` (1710 LOC) — heavyweight integration tests; 11+ `#[tokio::test]` cases exercising each tool against a seeded SQLite database with `RecordingProvider` LLM substitutes and a stub `FiligreeLookup` (`association` builder at line 573). + +**Dependencies:** + +- Inbound: `clarion-cli` (only — `crates/clarion-cli/src/serve.rs` is the sole consumer of the public API: `McpConfig::from_path`, `select_provider_with_env`, `FiligreeHttpClient::from_config`, `ServerState::new` + builders, `serve_stdio_with_state_on_runtime`). +- Outbound: + - `clarion-core` — `EdgeConfidence`, `INFERRED_CALLS_PROMPT_VERSION`, `InferredCallsPromptInput`, `LEAF_SUMMARY_PROMPT_TEMPLATE_ID`, `LeafSummaryPromptInput`, `LlmProvider`, `LlmProviderError`, `LlmPurpose`, `LlmRequest`, `LlmResponse`, `build_inferred_calls_prompt`, `build_leaf_summary_prompt`; transport `plugin::{ContentLengthCeiling, Frame, TransportError, read_frame, write_frame}` (`lib.rs:11–21`). + - `clarion-storage` — 20 symbols (`lib.rs:22–30`): types `CallEdgeMatch`, `EntityRow`, `InferredCallEdgeRecord`, `InferredEdgeCacheEntry`, `InferredEdgeCacheKey`, `InferredEdgeWriteStats`, `ReaderPool`, `StorageError`, `SummaryCacheEntry`, `SummaryCacheKey`, `UnresolvedCallSiteRow`, `WriterCmd`; functions `call_edges_from`, `call_edges_targeting`, `candidate_entities_for_unresolved_sites`, `child_entity_ids`, `contained_entity_ids`, `entity_at_line`, `entity_by_id`, `find_entities`, `inferred_edge_cache_key_id`, `inferred_edge_cache_lookup`, `normalize_source_path`, `summary_cache_lookup`, `unresolved_call_sites_for_caller`, `unresolved_callers_for_target`. + - External crates: `tokio` (mpsc/oneshot/broadcast, current-thread runtime, `spawn_blocking`), `serde` / `serde_json`, `serde_norway` (YAML), `reqwest::blocking` (Filigree HTTP), `rusqlite` (one direct `prepare` for `reference_neighbors` at line 2378 — the only raw SQL in this crate; everything else routes through `clarion-storage` helpers), `thiserror`. + +**Patterns Observed:** + +- **Read-side dispatch is genuinely thin.** Six of the seven tools (`entity_at`, `find_entity`, `callers_of` non-inferred, `execution_paths_from` non-inferred, `neighborhood` non-inferred, `issues_for`) call a `clarion-storage` helper through `ReaderPool::with_reader`, then envelope the result. Transformation done in `clarion-mcp` is narrow: building tool envelopes (`ok` / `result` / `error` / `diagnostics` / `truncated` / `truncation_reason` / `stats_delta`), shaping `entity_json` / `caller_json` / `callee_json` / `path_json` projections, and the `IssuesForAccumulator` drift classifier. The one substantive in-crate transform is `inferred_records_from_result` (2216–2266) which parses LLM JSON into `InferredCallEdgeRecord` and joins it back against the unresolved-site rows by `site_key`. +- **LLM dispatch lives in this crate, not in `clarion-core`.** `clarion-core` provides prompt templates, the `LlmProvider` trait, and request/response types. The MCP layer owns: cache lookup (`summary_cache_lookup`, `inferred_edge_cache_lookup`), cache-staleness checks (`stale_semantic`, `summary_cache_expired`, ADR-007 five-tuple key in `read_summary_inputs:1010–1016`), the budget ledger (`BudgetReservation` with RAII rollback on drop), the in-flight dispatch coalescer (`inferred_inflight` keyed by `InferredEdgeCacheKey`, 60s timeout), prompt construction, provider invocation (`spawn_blocking` to bridge to the sync provider trait), and the writeback via `WriterCmd::{UpsertSummaryCache, TouchSummaryCache, InsertInferredEdges}`. +- **Filigree integration is genuinely enrich-only.** Three independent skip paths route to `issues_unavailable` (lines 589–594, 619–628), which returns `ok=true` with `available=false` and a `reason` enum (`filigree-disabled` / `filigree-unreachable` / `filigree-client-error` / `entity-not-found`). The other six tools have no Filigree dependency. `FiligreeHttpClient::from_config` returns `Ok(None)` when disabled (filigree.rs:68–70) — disabled is the default. No code path makes a Filigree response required for the tool to succeed; this matches Loom federation §3 (`docs/suite/loom.md`). +- **Confidence-tier opt-in (ADR-028).** `optional_confidence` (1861–1872) defaults to `Resolved`. `inferred` is the only tier that triggers LLM dispatch (via `ensure_inferred_for_target` / `ensure_inferred_for_caller`). `ambiguous` is read-only over existing static-edge rows. +- **Writer-actor handoff.** All mutating storage operations go through `mpsc::Sender` + a `oneshot::Sender>` ack (`send_writer`, 1157–1171). Translates `WriterGone` / `WriterNoResponse` storage errors into retryable tool envelopes. ADR-011 compliance. +- **Stateful and stateless entry points co-exist.** The stateless `handle_json_rpc` (line 154) + `handle_tool_call` (line 1701) pair always emits `tool-unimplemented` envelopes for every tool; the stateful `ServerState::handle_json_rpc` (line 228) is the real dispatcher. The stateless path remains usable for `initialize` / `tools/list` and is exercised by unit tests inside the file. +- **Truncation contract** — every list-shaped success envelope can carry `truncation_reason: "edge-cap" | "issue-cap" | "entity-cap"`. `execution_paths_from` enforces `execution_edge_cap` (default 500); `issues_for` enforces a hardcoded 100-issue cap (line 631) and a 1000-contained-entity cap (`read_issues_for_entities:655`). +- **Time normalisation as plain math.** No `chrono` / `time` dependency — `default_now_string` emits `unix:{seconds}`, `timestamp_day_index` accepts either `unix:N` or ISO `YYYY-MM-DD…` prefix, and `days_from_civil` is the Howard Hinnant algorithm inline (2306–2314). + +### Tool table + +| Tool | Required inputs | Optional inputs | Primary storage helper | LLM dispatch path | +|------|------------------|------------------|-------------------------|--------------------| +| `entity_at` | `file: string`, `line: int ≥ 1` | — | `entity_at_line` (after `normalize_source_path`) | No | +| `find_entity` | `pattern: string` | `limit: 1..=100` (default 20), `cursor: string\|null` (numeric offset) | `find_entities` | No | +| `callers_of` | `id: string` | `confidence: resolved\|ambiguous\|inferred` (default `resolved`) | `call_edges_targeting` + `entity_by_id` | Only when `confidence=inferred` → `ensure_inferred_for_target` | +| `execution_paths_from` | `id: string` | `max_depth: 1..=8` (default 3), `confidence` (default `resolved`) | `call_edges_from` + `PathTraversal` (resolved/ambiguous) or `inferred_execution_paths` (inferred) | Only when `confidence=inferred` → bounded BFS of `ensure_inferred_for_caller` per node | +| `summary` | `id: string` | — | `summary_cache_lookup` then `WriterCmd::TouchSummaryCache` / `UpsertSummaryCache` | **Yes** — leaf-scope (ADR-030), `LlmPurpose::Summary`, max_output_tokens 512 | +| `issues_for` | `id: string` | `include_contained: bool` (default true) | `entity_by_id` + `contained_entity_ids` (cap 1000) | No — Filigree HTTP per entity via `spawn_blocking` | +| `neighborhood` | `id: string` | `confidence` (default `resolved`) | `entity_by_id` + `call_edges_targeting` + `call_edges_from` + `child_entity_ids` + `reference_neighbors` | Only when `confidence=inferred` → both `ensure_inferred_for_target` *and* `ensure_inferred_for_caller` (lines 528–534) | + +### LLM cache-key dispatch table + +| Path | Cache key tuple (ADR-007) | Source line | +|------|----------------------------|-------------| +| Summary | `entity_id` + `content_hash` + `prompt_template_id = LEAF_SUMMARY_PROMPT_TEMPLATE_ID` + `model_tier` (from `LlmProvider::tier_to_model("summary")`) + `guidance_fingerprint = "guidance-empty"` | `lib.rs:1010–1016` | +| Inferred edges | `caller_entity_id` + `caller_content_hash` + `model_id` (from `tier_to_model("inferred_edges")`) + `prompt_version = INFERRED_CALLS_PROMPT_VERSION` | `lib.rs:816–821` | + +On miss, both paths reserve via `BudgetLedger` (token-pessimistic, ceiling default 1_000_000 input+output combined), invoke the provider on `spawn_blocking`, commit actual tokens (or flip `blocked=true`), and on success write back via the writer-actor. Subsequent dispatches for the same key short-circuit through the in-flight coalescer (`coalesced_inferred_dispatch`, 865–908) which `broadcast::subscribe`s and waits up to 60 s. + +**Concerns:** + +- **`lib.rs` is 2620 LOC in one file.** Discovery question #1 — internal structure is *coherent* (clear bands: protocol surface → `ServerState` → per-tool handlers → LLM pipelines → transport loop → helpers), but the file is large enough to warrant subdivision on size grounds alone. The `IssuesForAccumulator`, the LLM inferred-edges pipeline (719–995), the LLM summary pipeline (997–1155), the budget ledger (1180–1316), and the envelope/projection helpers (1874–2400) are each plausible standalone modules. The current single-file layout is not a god-file in the architectural sense — each band has a single responsibility — but the size will degrade code-review velocity and grep ergonomics. +- **Dead stateless `handle_tool_call` stub** (`lib.rs:1701–1736`): emits `tool-unimplemented` envelopes for every tool name. Reachable only via the stateless `handle_json_rpc` (154) and `handle_frame` (1621) paths. `handle_frame` is exercised by one unit test (2542–2560) and is exported from the crate, so any external consumer that wires the stateless path will get permanently-broken `tools/call` responses. Not a runtime defect inside the CLI (which uses `handle_frame_with_state`), but a footgun in the public API. +- **`reference_neighbors` (lib.rs:2363–2400)** issues raw SQL against the `edges` table directly, bypassing the `clarion-storage` helper layer. It is the *only* place in this crate that does so. This creates a hidden coupling to the `edges` schema (`kind = 'references'`, `confidence`, `source_byte_start`, `source_byte_end`) outside the storage crate. If the schema changes, `clarion-storage` callers and tests will catch it but this function will not. +- **`InferredCallsResponseEdge::confidence: Option` field is parsed but unused for envelope shape** (lib.rs:1601–1607, used in 2247–2255). The model's reported confidence is stored as a property in the inferred-edge row's `properties_json`, but the storage layer does not surface it back through `caller_json`/`callee_json` — the tool envelope only exposes `edge_confidence` (the tier: resolved/ambiguous/inferred). The model's per-edge confidence is therefore preserved on disk but not queryable; consumers needing the score must hand-parse `properties_json`. +- **Coalesced-dispatch waiters get a generic stats delta when the leader fails.** `InferredDispatchOutcome::from_result` (1574–1595, used at 902–908) broadcasts a clonable outcome; non-leader waiters that receive a failure outcome surface it as their own (line 884–887). Acceptable, but the leader's diagnostics (e.g. `CLA-LLM-INVALID-JSON` usage block) are visible to the leader only; waiters see the failure code/message but lose the per-response diagnostics array. Minor observability gap. +- **`source_excerpt` (lib.rs:2151)** uses `std::fs::read_to_string` on the *current on-disk file path* to build LLM prompt input. This is *not* the content hash that keyed the cache; the file may have changed between the time the entity was scanned and the time the tool runs. The cache key still uses the stored `content_hash`, so a stale read here produces a cache miss with a fresh-but-misaligned prompt. The `stale_semantic` flag covers structural drift (caller_count / fan_out) but not source-text drift. Documented as a known v0.1 trade-off in the surrounding code? — no comment found. +- **`BudgetLedger::blocked` is sticky for the lifetime of the `ServerState`**: once any reservation overshoots, `blocked` flips to `true` (1196, 1296) and every subsequent LLM tool returns `token-ceiling-exceeded` until process restart. No reset path; no way to lift the ceiling without dropping the state. Matches a session-token semantic but is undocumented in the public API. +- **`FiligreeConfig::actor` blank handling**: `FiligreeHttpClient::associations_for` only sets the `x-filigree-actor` header when the actor string is non-blank (filigree.rs:94–96); Filigree currently requires the header for some endpoints. Silent omission rather than rejection at config-load. +- **No `Drop` cleanup for in-flight broadcast senders on leader cancellation.** If the leader task panics or is dropped *before* reaching the explicit `remove` at line 904, the `inferred_inflight` entry leaks until the next dispatch for the same key. `broadcast::Sender` itself is not a resource leak, but the map entry blocks subsequent dispatches from claiming leadership; subsequent callers will subscribe to a now-dead sender and time out at 60 s. Low-probability but present. + +### Confidence Assessment + +**Confidence:** High — Read 100% of `config.rs` (352 lines), 100% of `filigree.rs` (238 lines), 100% of the `lib.rs` declarations/dispatch (1–1700) and the helper/test bands (1700–2620). Sampled five handler bodies in full (`tool_entity_at`, `tool_find_entity`, `tool_callers_of`, `inferred_execution_paths`, `tool_issues_for`, `tool_summary`) and the LLM pipelines (`ensure_inferred_for_caller` through `perform_inferred_dispatch`). Cross-verified inbound dependency by reading `clarion-cli/src/serve.rs` (137 lines). Cross-verified outbound dependency claims against the `use` block at `lib.rs:11–34`. Cross-verified ADR alignment by quoting cache-key construction sites (5-tuple at 1010–1016, 4-tuple at 816–821) and ADR-028 default in `optional_confidence` (1864). + +### Risk Assessment + +- **Size-induced review burden** (lib.rs 2620 LOC) — Medium operational risk; not a correctness risk. The internal banding makes incremental refactors safe. +- **Dead stateless `handle_tool_call` stub in public API surface** — Low surface but high blast radius for any external consumer. Single fix: either remove from public exports or make it forward to the same handlers as the stateful path. +- **`reference_neighbors` raw SQL** — Schema-coupling risk; would not be caught by `clarion-storage` integration tests. +- **`source_excerpt` reads live disk, not the hashed snapshot** — Correctness drift risk under concurrent file modification; affects prompt fidelity but not cache correctness. +- **Sticky budget ledger** — Operational risk: process restart required after one ceiling breach. Acceptable for v0.1 / session semantics. +- **Filigree enrich-only contract** — Verified clean. Discovery question #5 answered: no Filigree code path is load-bearing. + +### Information Gaps + +- The Sprint-2 e2e script `tests/e2e/sprint_2_mcp_surface.sh` was not read in this pass (out of scope per task framing); coverage of the seven tools end-to-end is documented as "presumed" in `01-discovery-findings.md:138`. +- The integration tests at `tests/storage_tools.rs` (1710 LOC) were enumerated but not read in full; the `RecordingProvider` plumbing and the `state_for_filigree` stub were sampled to confirm they exist (lines 244–252). +- ADR text for ADR-007/028/029/030 was not re-opened in this pass; alignment claims rely on the cache-key/confidence-tier code matching the documented intent paraphrased in the task brief. +- The model's per-edge `confidence: Option` field is parsed from LLM output but not surfaced in tool responses — whether this is intentional (ADR-028 tiers are coarse-grained on purpose) or a documentation gap was not verified against the ADR. + +### Caveats + +- The "thin dispatch" characterisation is true for the six read-only tools but does not apply to the LLM-dispatch paths (`tool_summary` plus the `confidence=inferred` branches of `callers_of` / `execution_paths_from` / `neighborhood`), which carry substantive in-crate logic: cache-key construction (ADR-007), budget reservation, in-flight coalescing, prompt construction via `clarion-core` helpers, provider invocation on `spawn_blocking`, JSON-shape validation, and writeback via the writer-actor. +- The LOC band offsets cited in the catalog were computed from the on-disk `lib.rs` and are stable against the working tree at the time of analysis; minor drift (the file grew by 171 lines during B.8 per `01-discovery-findings.md:323`) means line numbers in this section are post-B.8. +- "MCP protocol revision `2025-11-25`" is sourced from the in-code constant (`lib.rs:36`); whether that matches the upstream MCP spec revision identifier was not independently verified. +- The Filigree HTTP client uses `reqwest::blocking` despite living in an otherwise async crate — calls are wrapped in `tokio::task::spawn_blocking` at `lib.rs:613`. Not a defect, but worth flagging if the crate is ever migrated to an async Filigree client. +## clarion-cli + +**Location:** `crates/clarion-cli/` + +**Responsibility:** Glue binary for the `clarion` executable; `clap`-driven subcommand dispatch (`install`, `analyze`, `serve`) that wires `clarion-core` (plugin host, LLM provider), `clarion-storage` (writer-actor + reader-pool), and `clarion-mcp` (stdio server) into a single end-user tool, and converts the storage layer's `RunStatus` taxonomy into shell exit codes. + +**Key Components:** + +- `src/main.rs` (33 lines) — process entry. Loads `.env` via `dotenvy::dotenv()` from CWD or any ancestor *before* `init_tracing()` so a `.env`-supplied `RUST_LOG` is in effect by the time the `EnvFilter` is built (commit `dc9bf41`, `main.rs:16–17`). Parses `cli::Cli`, then dispatches: `Install` and `Serve` run synchronously, `Analyze` builds an ad-hoc multi-thread `tokio::runtime::Builder` and `block_on`s `analyze::run(path)` (`main.rs:21–26`). No top-level runtime — each subcommand owns its own concurrency story. + +- `src/cli.rs` (43 lines) — `clap` derive structs only. `Install { --force, --path=. }`, `Analyze { path=. }`, `Serve { --path=., --config=Option }`. `--force` is declared but documented in code as "not implemented in Sprint 1" (`cli.rs:17–18`). + +- `src/install.rs` (168 lines) — `.clarion/` bootstrap. Refuses if the dir already exists (`install.rs:104–110`); refuses if `--force` is passed because Sprint-1 never implemented overwrite (`install.rs:87–92`). On `mkdir` success delegates to `populate_after_mkdir`, which (a) opens `clarion.db`, applies `clarion_storage::pragma::apply_write_pragmas` then `clarion_storage::schema::apply_migrations` (`install.rs:162–167`), (b) writes a stub `config.json` (`schema_version: 1, last_run_id: null`, `install.rs:22–26`), (c) writes a `.gitignore` carrying ADR-005's tracked-vs-excluded rules (`install.rs:54–77`), (d) writes a substantive `clarion.yaml` stub at project-root with LLM and Filigree-integration scaffolding (`install.rs:28–52`). Crucially, `clarion.yaml` is left untouched if it already exists (`install.rs:150–158`). Includes a cleanup guard: any failure inside `populate_after_mkdir` triggers `fs::remove_dir_all(.clarion)` before bubbling the error so the next attempt isn't blocked by the existence check (`install.rs:117–127`; references issue `clarion-ed5017139f`). + +- `src/serve.rs` (136 lines) — MCP stdio server wiring, in this exact sequence (`serve.rs:14–91`): (1) assert `.clarion/clarion.db` exists or hint the operator to run `install` first (`serve.rs:15–21`); (2) canonicalise the project root; (3) read `clarion.yaml` via `McpConfig::from_path` or default to `McpConfig::default()` (`serve.rs:26–33`); (4) resolve provider selection via `select_provider_with_env` with a `std::env::var` closure (`serve.rs:34`); (5) build the `Arc` via local `build_llm_provider` — `Disabled`/`Recording` (loads JSON fixture from `config.llm.recording_fixture_path` relative to project_root, `serve.rs:122–136`) / `OpenRouter` (passes `api_key`, `allow_live_provider: true`, model id, endpoint, and the attribution Referer/Title); (6) build the optional `FiligreeHttpClient::from_config` (`serve.rs:36–39`); (7) lock `stdin`/`stdout` and wrap stdin in `BufReader`; (8) build a **single-thread current-thread** tokio runtime, `runtime.enter()` as a guard so spawned tasks attach; (9) open the `ReaderPool` (size 16, `serve.rs:50`); (10) construct `ServerState::new(project_root, readers)`; (11) if a provider exists, spawn an LLM-only `Writer` against the same db_path with `DEFAULT_BATCH_SIZE`/`DEFAULT_CHANNEL_CAPACITY` and attach it via `state.with_summary_llm(writer.sender(), config.llm.clone(), provider)` (`serve.rs:55–65`); (12) if the Filigree client built, attach via `state.with_filigree_client(Arc::new(client))` (`serve.rs:66–68`); (13) hand off to `clarion_mcp::serve_stdio_with_state_on_runtime` (`serve.rs:70–72`); (14) drop `state`, drop `llm_writer` to close its sender, `runtime.block_on(handle)` to join the writer (`serve.rs:73–84`); (15) propagate `serve_result?` then the writer's `result?` so a clean MCP loop still fails the process if the writer errored. + +- `src/analyze.rs` (1436 lines) — the orchestrator. Internal structure, in source order: + + - **Public entry `pub async fn run(project_path: PathBuf)` (`analyze.rs:40–542`)** — single ~500-line function flagged `#[allow(clippy::too_many_lines)]`. Phases (clearly demarcated by `── … ──` banner comments): + 1. Path validation + `.clarion/` existence check (`:41–56`). + 2. **Writer actor lifecycle — open**: `Writer::spawn(db_path, DEFAULT_BATCH_SIZE, DEFAULT_CHANNEL_CAPACITY)` returns a `(writer, handle)` pair; mints a `Uuid::new_v4()` run id and `BeginRun` via `writer.send_wait(...)` (`:60–75`). + 3. **Plugin discovery** via `clarion_core::discover()`; successes pushed into `plugins`, failures collected into `discovery_errors` (`:78–97`). + 4. **No-plugins branch** (`:99–171`): distinguishes "zero discovered + zero errors" (`SkippedNoPlugins` via `CommitRun`, exits 0 with a "skipped_no_plugins" stdout line) from "zero usable + non-empty errors" (`FailRun` with the concatenated error list, then `bail!` for non-zero exit). The fix for hiding manifest-parse bugs as `SkippedNoPlugins` is explicit in the comment at `:100–103`. + 5. **Extension union + source walk** — collect_source_files walks once over the union of every plugin's declared extensions (`:174–184`). + 6. **Per-plugin loop** (`'plugins:` label, `:211–412`): filter the global file list to this plugin's extensions; if empty, `continue`. Otherwise dispatch a `tokio::task::spawn_blocking(move || run_plugin_blocking(...))` and route its `JoinResult` through `handle_plugin_task_join_result` (which normalises a `JoinError` panic into a crash-reason string rather than `?`-propagating, `:259–271`, regression-tested as `clarion-cf17e4e779`). On `Err(reason)`: push into `crash_reasons`, tick `CrashLoopBreaker::record_crash`, and `break 'plugins` if `CrashLoopState::Tripped` (`:274–292`). On `Ok(BatchResult { entities, edges, unresolved_call_sites, stats, findings })`: fold per-batch stats into per-run accumulators; log every `HostFinding` individually (`:312–327`); flush entities then unresolved call-site replacements (`WriterCmd::ReplaceUnresolvedCallSitesForCaller`) then edges to the writer-actor in that exact order (`:341–391`). Any writer `send_wait` error stops the per-plugin loop and sets `run_outcome = HardFailed { reason }` (`:392–402`). + 7. **`RunOutcome` resolution** (`:421–522`) — `enum RunOutcome { Completed, SoftFailed { reason }, HardFailed { reason } }` at `:558–563`. Promotion rule: `Completed` + non-empty `crash_reasons` → `SoftFailed` so the entity batch still commits *and* the run row marks failed (`:421–429`). Snapshots `writer.dropped_edges_total` and `writer.ambiguous_edges_total` (atomic counters held on the `Writer` handle) and `pyright_latency.p95_ms()` into the stats JSON (`:435–441`). The three terminal branches dispatch: + - `Completed` → `WriterCmd::CommitRun { status: RunStatus::Completed, … }` + - `SoftFailed { reason }` → `WriterCmd::CommitRun { status: RunStatus::Failed, … }` plus `"failure_reason": reason` in the stats JSON; the writer folds `UPDATE runs SET status='failed'` into the open entity tx so the partial work commits atomically with the failure marker (`:478–509`, comment at `:551–553`). + - `HardFailed { reason }` → `WriterCmd::FailRun` — rolls back the open tx (`:510–521`). + 8. **Writer-actor lifecycle — close**: `drop(writer)` closes the command channel; `handle.await` joins the actor task (`:524–528`); on any `fail_reason`, `bail!` for non-zero exit — the run row is already correctly marked, this is purely about surfacing failure to the shell (`:530–534`). + + - **`run_plugin_blocking` (`:646–759`)** — synchronous worker that `spawn_blocking` runs. Spawns the plugin via `PluginHost::spawn`; loops `host.analyze_file(file)` for each file in the per-plugin extension-filtered list; accumulates entities, edges, per-file `AnalyzeFileStats`, and per-file unresolved call sites; on the happy path tries `host.shutdown()` and falls back to `child.kill()` if shutdown writes to a closed pipe (`:731–742`); always `reap_and_classify_exit(&mut child, ...)` afterwards because `std::process::Child::Drop` does not `wait()` on Unix and would leak zombies (`:746–747`, comment at `:641–645`). + + - **`reap_and_classify_exit` (`:769–815`)** — on `signal() == SIGKILL (9)` or `SIGSEGV (11)` appends `HostFinding::oom_killed(plugin_id, signal)` per ADR-021 §2d; other signals or non-zero exits get a `warn` log but no finding. + + - **`classify_host_error` (`:818–843`)** — the explicit `HostError` → `String` mapping for fail-run reasons. Match arms: `EntityCapExceeded(_)` ("exceeded entity-count cap"), `PathEscapeBreakerTripped` ("tripped path-escape breaker"), `Spawn(msg)`, `Handshake(me)`, `Transport(te)`, `Protocol(pe)` (formats `code` + `message`), wildcard `other`. + + - **Entity/edge mapping** (`:846–946`) — `map_entity_to_record` derives `short_name` by rsplit('.'), serialises `entity.raw.extra` into `properties_json`, computes `content_hash` via local `content_hash_for_entity` (BLAKE3 over full file bytes for `module` kind, over normalised joined source lines `[start_line-1..end_line]` otherwise — `:907–927`). `map_edge_to_record` is a near-direct field-copy. Worth noting: `source_byte_start`/`source_byte_end` are hard-coded to `None` on entities — only the line range is captured. Edges keep byte ranges. + + - **Unresolved call-site bookkeeping (B.4*)** (`:948–1055`) — `map_unresolved_call_sites_for_file` groups sites by caller; checks "authoritative" mode (where `stats.unresolved_call_sites_total == stats.unresolved_call_sites.len()`) and pre-creates empty `PendingUnresolvedCallSites` for every function entity in the batch so the writer's `ReplaceUnresolvedCallSitesForCaller` can clear stale rows for callers that no longer have any unresolved sites. `validate_unresolved_call_site` enforces non-negative ordinal, non-empty/`<=512`-byte callee_expr, monotone byte range. `unresolved_call_site_key` is a BLAKE3 of `caller_entity_id || start_be || end_be || callee_expr`. + + - **Source-tree walk** (`:1063–1170`) — `walk_dir` is hand-rolled `std::fs::read_dir` recursion (no `walkdir` dep), with `SKIP_DIRS = [".clarion",".git",".hg",".svn",".jj",".venv","__pycache__","node_modules"]`, symlink skipping, and per-entry I/O error counting (skipped entries are tallied and surfaced as one summary `warn` line at end of walk to avoid silent partial analysis). **Does not honour `.gitignore`** — flagged P4 at `:1078`. + + - **Time helpers** (`:1180–1220`) — hand-rolled `iso8601_now()` using Howard Hinnant's `civil_from_days`, to avoid bringing in `chrono` for one format string. + +- `src/stats.rs` (37 lines) — `pub(crate) struct P95Accumulator { samples_ms: Vec }` with `record_many` and a nearest-rank `p95_ms()` (`stats.rs:21`). Sole client is the pyright-query-latency rollup in `analyze.rs`. + +**Integration tests** (`crates/clarion-cli/tests/`, 1217 LOC total): +- `install.rs` (247 lines) — black-box `assert_cmd` cases covering `.clarion/` contents, `.gitignore` rule presence, refusal-on-existing, `--force` refusal. +- `analyze.rs` (389 lines) — black-box analyze coverage. +- `serve.rs` (213 lines) — runs `clarion serve` as a child process, frames JSON-RPC bodies via `clarion_core::plugin::{Frame, read_frame, write_frame}` (re-exported through the `plugin` facade for test consumers), exercises the MCP `initialize` round-trip and `summary` tool dispatch (it imports `LEAF_SUMMARY_PROMPT_TEMPLATE_ID`). +- `wp1_e2e.rs` (74 lines) — WP1 walking-skeleton; mostly install/analyze sanity. +- `wp2_e2e.rs` (494 lines) — WP2 walking-skeleton consuming the on-disk `clarion-plugin-fixture` binary (declared as a `[dev-dependencies]` workspace member in `Cargo.toml:33`). + +**Dependencies:** + +- Inbound: + - End-users / shell / CI (the binary). + - `tests/e2e/sprint_1_walking_skeleton.sh` and `tests/e2e/sprint_2_mcp_surface.sh` invoke it as a subprocess. + - `tests/perf/b8_scale_test/driver.py` (B.8 scale-test harness) invokes it as a subprocess. + - No Rust-level inbound deps — this is a `[[bin]]`-only crate and exposes no library API (`Cargo.toml:12–14`). + +- Outbound: + - `clarion-core` — `PluginHost`, `discover`, `Manifest`, `DiscoveredPlugin`, `AcceptedEntity`/`AcceptedEdge`, `AnalyzeFileOutcome`, `AnalyzeFileStats`, `UnresolvedCallSite`, `CrashLoopBreaker`/`CrashLoopState`, `HostError`, `HostFinding`, `FINDING_DISABLED_CRASH_LOOP`, `LlmProvider`, `OpenRouterProvider`/`OpenRouterProviderConfig`, `Recording`/`RecordingProvider` (used in `analyze.rs:19–23`, `serve.rs:7–9`). + - `clarion-storage` — `Writer`, `ReaderPool`, `WriterCmd`, `EntityRecord`, `EdgeRecord`, `RunStatus`, `UnresolvedCallSiteRecord`, `DEFAULT_BATCH_SIZE`/`DEFAULT_CHANNEL_CAPACITY`, `pragma`, `schema` (used in `analyze.rs:24–27`, `install.rs:20`, `serve.rs:12`). + - `clarion-mcp` — `ServerState`, `config::{McpConfig, ProviderSelection, select_provider_with_env}`, `filigree::FiligreeHttpClient`, `serve_stdio_with_state_on_runtime` (used in `serve.rs:10–11, 52, 71`). + - Third-party: `clap` (derive CLI), `tokio` (runtime + `spawn_blocking` + `block_on`), `anyhow` (error type), `tracing` + `tracing-subscriber` (with `EnvFilter`), `dotenvy` (env loading), `uuid` (run IDs), `blake3` (content hashes + unresolved-site keys), `rusqlite` (install-time direct connection only — analyze and serve go through `Writer`/`ReaderPool`), `serde_json`. + +**Patterns Observed:** + +- **Pattern A buffering** (documented at `analyze.rs:7`): plugin work runs synchronously inside `spawn_blocking`, returns a `BatchResult` to the async caller, and only then does the caller emit `WriterCmd::Insert{Entity,Edge}` over the writer-actor channel. The blocking task never touches the writer directly. +- **Tri-state run outcome** (`Completed` / `SoftFailed` / `HardFailed`): explicitly distinguishes "plugin crashed but other plugins' entities should still persist" (SoftFailed → `CommitRun(Failed)`) from "writer-actor itself is broken" (HardFailed → `FailRun`). Comment at `:543–556` is load-bearing — the chosen WriterCmd differs by branch. +- **Atomic claim+transition style errors**: `JoinError` is *not* `?`-propagated; it's intercepted by `handle_plugin_task_join_result` and reshaped into a crash reason so the run-row resolution machinery still fires. The bypass regression is named in code (`clarion-cf17e4e779`) at `:1230–1236`. +- **Best-effort cleanup with auditable fallback**: `install.rs` removes a partial `.clarion/` on bootstrap failure and logs (not bails) if cleanup itself fails; `analyze.rs::run_plugin_blocking` always reaps the child even on the kill path. +- **Single-thread current-thread runtime for stdio loops, multi-thread for analyze**: `serve.rs:45–48` deliberately uses `Builder::new_current_thread()` (the stdin loop is the only thing actually running); `main.rs:22–25` uses `new_multi_thread` for analyze because `spawn_blocking` needs a worker thread. +- **Direct schema apply in install, writer-actor everywhere else**: `install.rs` opens its own `rusqlite::Connection` to run pragmas + migrations (the writer-actor doesn't exist yet at install time); after that, every write goes through `WriterCmd::*`. +- **Stats JSON is structured but stringified**: `CommitRun.stats_json` is built via `serde_json::json!` and then `.to_string()` (`analyze.rs:452–465`), matching `clarion-storage`'s `String` field signature. + +**Concerns:** + +- **`analyze::run` is a single ~500-line `async fn` with `#[allow(clippy::too_many_lines)]` at `:39`.** It mixes plugin discovery, file walking, per-plugin orchestration, writer-actor lifecycle, crash-loop policy, and three-way outcome resolution. The phase banners (`── Writer actor ──`, `── Discover plugins ──`, etc.) prove the author recognised the seams; extracting at least the per-plugin loop and the outcome-resolution match into named helpers would reduce the cognitive cost and make adding a fourth `RunOutcome` variant safer. +- **`source_byte_start` / `source_byte_end` are hard-coded `None` on entity records** (`analyze.rs:873–874`). The schema columns exist (`EntityRecord` carries them) and edges do populate them. Either the plugin should emit byte offsets and the CLI should plumb them, or the entity columns are documented dead weight. +- **Hand-rolled date math** (`civil_from_unix_secs`, `:1197–1220`) was justified for Sprint 1 by avoiding `chrono`. With `dotenvy`, `blake3`, `uuid`, and `tracing-subscriber` already in tree, the "we don't have a date dep" rationale is thinner now; the comment at `:1175–1179` itself anticipates promoting `chrono` "at that point." Worth a follow-up issue. +- **The source walk does not honour `.gitignore`** (P4 noted in-code at `:1078`). On the `elspeth` corpus this likely means walking generated and vendored code paths the operator considers out-of-scope. `SKIP_DIRS` is a coarse stopgap. +- **`install.rs::initialise_db` opens a connection, applies pragmas + migrations, and lets it drop without an explicit close.** SQLite handles this safely (the dtor closes the handle and flushes WAL), but the symmetry with the writer-actor's explicit `Drop` and the explicit ordering elsewhere makes this stand out. Not a defect; a stylistic gap. +- **Serve's LLM writer is independent from the analyze writer.** When `clarion serve` is up *and* `clarion analyze` is run in another process, two `Writer` actors hold connections to the same `clarion.db`. The pragma layer (WAL + `busy_timeout`) is what keeps that safe — this is a `clarion-storage` invariant the CLI relies on but doesn't enforce or test in the cli-tests. Worth verifying in the storage subsystem brief. +- **`--force` accepted but unimplemented.** `install.rs:87–92` rejects the flag with a `bail!`. Sprint-2+ has not implemented the overwrite path despite the `cli.rs:17` doc-comment hinting at one. If the operator workflow has stabilised, either implement it or remove the flag. +- **No integration test exercises the `SoftFailed` path end-to-end.** `analyze.rs` tests cover `Completed` and `SkippedNoPlugins`; the soft-fail branch (where one plugin crashes but another succeeds) is the most subtle path — it's the one where an entity batch and a `status='failed'` UPDATE share a single SQLite transaction — and no `tests/analyze.rs` case (per a `grep` of the test file's signatures, not deep-read this pass) targets it. The crash-loop unit tests inside `analyze.rs:tests` cover `handle_plugin_task_join_result` but not the writer side of the soft-fail folding. + +**Confidence:** High — read `main.rs`, `cli.rs`, `install.rs`, `serve.rs`, `stats.rs`, and `Cargo.toml` in full; read `analyze.rs:1–542` (the full async `run`), `:559–815` (RunOutcome, JoinError helper, BatchResult/BatchStats/PendingUnresolvedCallSites structs, run_plugin_blocking, reap_and_classify_exit), `:818–843` (classify_host_error), `:846–946` (entity/edge mapping + content hashing), `:948–1055` (unresolved-call-site mapping), `:1057–1170` (source walk), and `:1180–1220` (time helpers). Cross-validated outbound deps by reading the import block at `analyze.rs:19–27`, `serve.rs:7–12`, `install.rs:20`; confirmed against `Cargo.toml:17–29`. Sample of test headers read for `tests/install.rs` and `tests/serve.rs`. Phase-level walkthrough of `analyze::run` annotated with line ranges throughout. The five open questions in the brief are answered in the text above with file:line citations. + +**Risk Assessment:** + +- **God-function risk on `analyze::run`** (high likelihood, medium impact). Length is already a documented smell. Mitigation: extract the per-plugin loop and outcome resolution; add `SoftFailed` integration coverage before extraction so the refactor has a regression net. +- **Stale CLI surface risk** (low likelihood, low impact). `--force` advertised but unimplemented; could mislead a CI author. Mitigation: implement or remove. +- **Multi-process writer correctness** (low likelihood, high impact). Two `Writer` actors against one DB rely on `clarion-storage` pragma discipline (WAL + `busy_timeout`). The CLI is the only place this combination is wired in production. Mitigation: a serve+analyze concurrent integration test would prove the invariant from the CLI side; right now the discipline is owned by `clarion-storage` and trusted by the CLI. + +**Information Gaps:** + +- `tests/analyze.rs` (389 lines) was not deep-read this pass; the claim that no test exercises the `SoftFailed` path is based on the test file's signature surface and the comments in `analyze.rs`, not on a function-by-function read. A follow-up could promote that claim from "likely" to "verified" or refute it. +- `select_provider_with_env`'s exact precedence (env-var override of YAML vs YAML wins) is `clarion-mcp::config`'s concern, not visible from CLI source. The CLI passes a `|name| std::env::var(name).ok()` closure (`serve.rs:34`) and trusts the resolver. +- Whether the LLM `Writer` spawned in `serve.rs` and the `analyze` `Writer` would conflict on the same `clarion.db` was not verified end-to-end — only that pragma discipline in `clarion-storage` is intended to absorb it. + +**Caveats:** + +- Line counts include `#[cfg(test)]` blocks where present in `src/`. `analyze.rs:1224+` contains an in-source `mod tests` whose contents were not deep-read beyond the `handle_plugin_task_join_result` regression comment. +- The `clarion.yaml` stub written by `install` (`install.rs:28–52`) commits the CLI to a specific config shape (model id `anthropic/claude-sonnet-4.6`, default Filigree port `8766`, default OpenRouter endpoint). Those defaults belong to the operator config story, not the CLI's responsibility surface — flagged here only as a fact, not a critique. +- No code-quality assessment is made — that is an `axiom-system-architect:assess-architecture` concern. +## Test-only Rust fixture plugin (`clarion-plugin-fixture`) + +**Location:** `crates/clarion-plugin-fixture/src/` + +**Responsibility:** Protocol-compatible stand-in for a real language plugin: a minimal Rust binary speaking the same Content-Length-framed JSON-RPC 2.0 protocol on stdin/stdout as the Python plugin, used by `clarion-core`'s `host_subprocess` integration test to exercise `PluginHost::spawn` end-to-end without bringing a Python interpreter and pyright into the test loop. + +**Key Components:** + +- `Cargo.toml` (19 lines) — declares a single `[[bin]]` target (`clarion-plugin-fixture`, `src/main.rs`); depends on `clarion-core` (path dep, version `0.1.0-dev`) and `serde_json` from the workspace; inherits workspace `[lints]`. No library is published. +- `src/main.rs` (128 lines, full code) — the entire plugin. One blocking `loop` over `read_frame(&mut reader, ContentLengthCeiling::DEFAULT)` (`main.rs:33`); per-frame `serde_json::from_slice` to a free-form `Value` so it can branch on `id`-presence (notification vs. request) before typed deserialisation (`main.rs:37-46`). Five method branches matching the L4 protocol surface: + - `initialize` (request) → `InitializeResult { name: "clarion-plugin-fixture", version: "0.1.0", ontology_version: "0.1.0", capabilities: {} }` (`main.rs:68-76`). + - `initialized` (notification) → state transition only, no reply (`main.rs:50-53`). + - `analyze_file` (request) → extracts `params.file_path` (or `""`), echoes it back inside one stub entity `{"id": "fixture:widget:demo.sample", "kind": "widget", "qualified_name": "demo.sample", "source": {"file_path": }}`, returns `AnalyzeFileResult { entities: vec![entity], edges: vec![], stats: default }` (`main.rs:77-108`). + - `shutdown` (request) → empty `ShutdownResult` (`main.rs:109-112`). + - `exit` (notification) → `std::process::exit(0)` (`main.rs:54-56`). +- `src/lib.rs` (3 lines) — comment-only stub explaining the crate is binary-only; exists so Cargo resolves the workspace member cleanly. + +**Dependencies:** + +- Inbound: `crates/clarion-core/tests/host_subprocess.rs` is the sole consumer — it locates the binary via `CARGO_BIN_EXE_clarion-plugin-fixture`, falling back to `/{debug,release}/clarion-plugin-fixture`; the manifest `tests/fixtures/plugin.toml` is `include_bytes!`-embedded at compile time (`host_subprocess.rs:16`). CI's `walking-skeleton` job builds this binary as part of `cargo build --workspace --bins` so the test can find it on disk (see `CLAUDE.md` build-commands section: "wp2_e2e tests need clarion-plugin-fixture on disk"). +- Outbound: `clarion-core::plugin::limits::ContentLengthCeiling` (the 8 MiB default), `clarion-core::plugin::transport::{Frame, read_frame, write_frame}` (the shared framing codec), `clarion-core::plugin::{AnalyzeFileParams, AnalyzeFileResult, AnalyzeFileStats, InitializeResult, JsonRpcVersion, ResponseEnvelope, ResponsePayload, ShutdownResult}` (the typed protocol structs); `serde_json` for the free-form `Value` pre-dispatch. + +**Patterns Observed:** + +- **Protocol-by-shared-types.** The fixture reuses `clarion-core`'s own protocol structs (`InitializeResult`, `AnalyzeFileResult`, `ResponseEnvelope`, …) for response serialisation — there is no parallel schema definition. A breaking change to `protocol.rs` therefore fails compilation of the fixture, not at runtime under test, which is the right ordering. +- **Same ceiling as production.** Frame reads use `ContentLengthCeiling::DEFAULT` (the ADR-021 §2b 8 MiB cap), with the source comment explicitly noting that `unbounded()` is now `#[cfg(test)]`-only (`main.rs:30-32`). The fixture lives under the same wire-cap discipline as a real plugin. +- **Fail-fast on protocol violations.** Every recoverable branch in a real plugin is `std::process::exit(1)` here — malformed frame, non-object body, missing/non-string `method`, integer-id parse failure, unknown method, params-deserialise failure (`main.rs:34, 39, 45, 57, 64, 90, 113`). Acceptable because the consumer is exclusively an integration test; the alternative would obscure protocol-violation bugs behind fixture-side error handling. +- **Notification vs. request branching on `id`-presence.** Reads the raw `Value` first, checks `id.is_some_and(|v| !v.is_null())` to decide whether the frame requires a response (`main.rs:42, 48-60`). This matches the JSON-RPC 2.0 spec and parallels the Python plugin's branching in `server.dispatch` (`server.py:239-261`). +- **Stable identity for assertions.** `plugin_id = "fixture"`, kind `"widget"`, and the literal entity ID `"fixture:widget:demo.sample"` are baked into the source — `host_subprocess.rs` asserts on this exact string, so the test signal is exact-match rather than parse-and-inspect. + +**Concerns:** + +- **No request-id sanity on `shutdown`.** Unlike the Python plugin, the fixture doesn't gate `analyze_file` on having received `initialized` — `state.initialized` doesn't exist. This is fine for the single happy-path test it supports, but means the fixture cannot exercise the host's `-32002 NOT_INITIALIZED` error path. If a future test wanted to assert that the host *itself* sequences the handshake correctly, it would have to verify host-side state rather than fixture-side rejection. +- **`exit(1)` on any malformed frame is observable only as a non-zero process exit.** The host-side test gets no structured signal about which branch failed. For an integration test fixture this is by design; flagging because anyone running the fixture by hand against a non-test client will see opaque exits. +- **No stderr discipline.** A real plugin (Python's `stdout_guard.py`) reserves stdout strictly for framing; the fixture relies on the absence of any `eprintln!` or `println!` in its own code rather than installing a guard. For a 128-line file with `serde_json` as the only output-side dep this is fine, but worth noting as a delta from the production-plugin pattern. + +**Confidence:** High — Read `main.rs` (128 lines, 100% of file), `lib.rs` (3 lines, 100%), `Cargo.toml` (19 lines, 100%); cross-verified consumer via `crates/clarion-core/tests/host_subprocess.rs` lines 3-7, 15-27, and 60-66 (binary-location strategy, fixture identity assertions, manifest constants). Cross-validated against `docs/arch-analysis-2026-05-18-1244/01-discovery-findings.md` §4 Subsystem E framing and `CLAUDE.md` layout summary. Protocol identity confirmed by the matching set of imports from `clarion_core::plugin::*` against the Python plugin's `server.py:7-19` docstring describing the same five methods and response shapes. Content-Length framing parity confirmed via the explicit `ContentLengthCeiling::DEFAULT` (8 MiB) source comment matching the Python `MAX_CONTENT_LENGTH = 8 * 1024 * 1024` at `server.py:48`. + +**Information Gaps:** + +- Did not read the upstream `clarion_core::plugin::transport` module to verify exactly how `read_frame` / `write_frame` interpret the ceiling; took the source comment at face value. +- Did not run `cargo build -p clarion-plugin-fixture` on the current branch to confirm the binary still compiles. Treated the unmodified `Cargo.toml` and the recent (b87bc1d) signoff record as sufficient evidence that the walking-skeleton CI job was green at sprint close. + +**Caveats:** + +- "Protocol-compat" here means *exact wire-shape compatibility* on the five L4 methods. The fixture does not exercise the `capabilities.wardline` probe shape, `parse_status` on module entities, `parent_id`/`contains` edges, calls/references resolution, the `stats` payload's `unresolved_call_sites`, or any of the Sprint-2 ontology surface. It is a *minimum*-shape test stand-in, not a feature-parity one. +- The fixture's `ontology_version = "0.1.0"` (`main.rs:72`) is deliberately the Sprint-1 baseline; this is the version against which the host's manifest-handshake validator is tested. It does *not* track the Python plugin's `0.5.0` and shouldn't. + +**Risk Assessment:** + +- *Drift between fixture and real plugins.* The fixture has been stable since Sprint 1 close and the protocol contract is enforced by shared `clarion-core` types, so the drift surface is bounded to behavioural-not-structural divergence (e.g. a real plugin adding handshake side-effects the fixture doesn't model). The host-side test exercises only the structural surface, so this is a known-acceptable gap. +- *Single-consumer dependency.* The fixture exists exclusively for `host_subprocess.rs`. If that test were retired, the fixture would become dead code; conversely, the test cannot be expanded to cover behaviours the fixture doesn't model without growing the fixture. Pre-existing carryover issue `clarion-adeff0916d` (fixture-binary self-build) tracks one known sharp edge here. +- *Build-ordering coupling.* The walking-skeleton CI job depends on `cargo build --workspace --bins` running before `cargo nextest run` so the binary is on disk when `host_subprocess.rs` looks for it. This is documented in `CLAUDE.md` and codified in `.github/workflows/ci.yml`'s `walking-skeleton` job, but is an implicit dependency that would break if a future contributor used `cargo nextest run --workspace` without the prior `cargo build`. +## Python language plugin (`plugins/python`) + +**Location:** `plugins/python/src/clarion_plugin_python/` + +**Responsibility:** Out-of-process language plugin that ingests a single Python source file at a time, extracts module/class/function entities plus `contains`/`calls`/`references` edges, and serves them to the Rust core over a Content-Length-framed JSON-RPC 2.0 channel on stdin/stdout (the L4 protocol). + +**Key Components:** + +- `__main__.py` (15 lines) — installs the stdout discipline guard, then delegates to `server.main()`; threads the server's exit code out to the host (`__main__.py:14`). +- `server.py` (285 lines) — L4 JSON-RPC dispatch loop. Implements the five protocol methods exactly as the Rust host's typed `protocol.rs` expects: `initialize`/`initialized`/`analyze_file`/`shutdown`/`exit` (`server.py:226-261`). Owns `ServerState` (initialized flag, shutdown flag, captured `project_root`, lazy `PyrightSession`) and the `read_frame`/`write_frame` Content-Length codec with an 8 MiB symmetric cap matching ADR-021 §2b (`server.py:48`, `71-126`). `handle_initialize` captures the host-supplied `project_root` and embeds the Wardline probe result in `capabilities.wardline` (`server.py:141-153`). `handle_analyze_file` reads the file off disk, lazily constructs the `PyrightSession`, and calls `extractor.extract_with_stats(...)` (`server.py:177-221`). +- `extractor.py` (744 lines, +98 on this branch for B.8) — AST → wire-shape extractor. `extract_with_stats` parses the source with `ast.parse`, prepends exactly one `module` entity (B.2 §3 Q1), then recursively walks via `_walk` to emit one `function` per `FunctionDef`/`AsyncFunctionDef` and one `class` per `ClassDef` (`extractor.py:261-344`, `_walk` at `589-668`). `parent_id` and one `contains` edge per non-module entity satisfy ADR-026 decision 2's dual encoding (`extractor.py:107-117`, `671-677`). `_ReferenceSiteCollector` is the separate `ast.NodeVisitor` pass for B.5* reference sites (`extractor.py:358-485`), then `extract_with_stats` hands the function IDs to `call_resolver.resolve_calls` and the reference sites to `reference_resolver.resolve_references` (`extractor.py:338-342`). Same-id collisions are handled at the emit boundary: `_has_overload_decorator` recognises `@overload` / `@typing.overload` / `@typing_extensions.overload` and skips emission *and* recursion entirely (`extractor.py:567-586`, `624`); any other duplicate (aliased overload imports, `@singledispatch.register def _():` runs) is dropped first-wins with a stderr line and a `duplicate_entities_dropped_total` bump (`extractor.py:629-637`). +- `pyright_session.py` (1251 lines) — long-running `pyright-langserver --stdio` LSP client. See sub-section below. +- `call_resolver.py` (64 lines) — `CallResolver` `Protocol` plus `CallsRawEdge` / `UnresolvedCallSite` / `Finding` TypedDicts; `NoOpCallResolver` is the test stand-in (`call_resolver.py:49-64`). `PyrightSession` is the production implementation. +- `reference_resolver.py` (69 lines) — symmetric: `ReferenceResolver` `Protocol`, `ReferenceSite` dataclass, `ReferencesRawEdge` TypedDict, `NoOpReferenceResolver` (`reference_resolver.py:54-69`). +- `entity_id.py` (75 lines) — Python side of the L2 byte-for-byte ADR-003+ADR-022 entity-ID assembler. Validates `plugin_id` / `kind` against the grammar `[a-z][a-z0-9_]*`, refuses the `:` separator inside any segment, raises typed `EmptySegmentError` / `GrammarViolationError` / `SegmentContainsColonError`. Cross-validated against `fixtures/entity_id.json` row-by-row (`entity_id.py:66-75`). +- `qualname.py` (46 lines) — ADR-018 L7 canonical qualname. Pure-AST reconstruction of CPython's runtime `__qualname__`: walks the parent chain in reverse, prepending `parent..` for function ancestors and `parent.` for class ancestors (`qualname.py:32-46`). Lock-in: this string must equal what Wardline produces for the same definition, otherwise the cross-product join breaks. +- `wardline_probe.py` (56 lines) — L8 fail-soft Wardline probe. `importlib.import_module("wardline.core.registry")` plus `importlib.import_module("wardline")`, then a `packaging.version` half-open range check against the manifest's `[integrations.wardline].min_version` / `max_version` (`wardline_probe.py:36-56`). Returns one of three dicts: `{"status": "absent"}`, `{"status": "enabled", "version": ...}`, `{"status": "version_out_of_range", "version": ...}`. **Invoked once per session at `initialize`** (`server.py:151`), never per-file. The `wardline.core.registry` import is the named Loom-doctrine asterisk from `docs/suite/loom.md` §5; Sprint 1 only proves the import + version-pin handshake — REGISTRY is not yet consumed. +- `stdout_guard.py` (62 lines) — replaces `sys.stdout` with a `_GuardedTextStdout` that raises `StdoutGuardError` on any write; captures the real `stdin.buffer` / `stdout.buffer` byte streams for the framing codec to use (`stdout_guard.py:57-62`). Single-shot, called by `__main__` before the dispatch loop starts. +- `__init__.py` (3 lines) — `__version__ = "0.1.4"`. + +**Sub-section: `pyright_session.py` (1251 lines, ~17% of total plugin LOC)** + +This file is the entire pyright integration surface. Internal structure: + +- *Public class `PyrightSession`* (`:117-758`) — implements both the `CallResolver` and `ReferenceResolver` Protocols. Constructed lazily once per `analyze_file` session by `server.handle_analyze_file` and held on `ServerState.pyright` for the lifetime of the connection (`server.py:193-194`, closed in `shutdown` handler at `server.py:246-248`). Public surface: `__init__`/`__enter__`/`__exit__`/`close`/`resolve_calls`/`resolve_references`/`kill_for_test`/`stderr_thread_alive`. Constructor knobs (`init_timeout_secs=30`, `call_timeout_secs=5`, `max_restarts_per_run=3`, `max_reference_sites_per_file=2000`) are exposed for tests (`pyright_session.py:118-145`). +- *Process lifecycle* — `_ensure_process` (`:505-516`) lazily spawns; `_start_process` (`:536-599`) does `subprocess.Popen([pyright-langserver, --stdio], cwd=project_root, env=..., stdin/stdout/stderr=PIPE)` and immediately calls `_initialize` with the LSP `initialize` request (`:601-616`). `_resolve_executable` (`:618-625`) walks: absolute-path → `sys.executable`'s sibling directory (i.e. the active venv) → `shutil.which`. A stderr-drain thread (`_start_stderr_drain` `:634-640`, `_drain_stderr` `:642-649`) keeps the 64 KiB `_stderr_tail` ring populated for diagnostics; the thread is daemonised. +- *Restart / poison handling* — `_record_restart_or_poison` (`:518-534`) increments `_restart_count` and emits a `CLA-PY-PYRIGHT-RESTART` finding; after 3 restarts the session goes `_disabled = True` and emits one `CLA-PY-PYRIGHT-POISON-FRAME`. Five fail-soft `CLA-PY-PYRIGHT-*` finding subcodes are defined at the top of the file (`:34-41`). +- *LSP transport* — `_request` (`:651-670`) writes Content-Length-framed JSON and busy-loops on `_read_message` skipping mismatched-id frames; `_notify` (`:672-674`) is the no-response variant; `_read_message` (`:693-714`) reads headers + body using `_read_line`/`_read_exact`/`_wait_readable` helpers (`:1218-1247`) that enforce a per-call deadline via `select.select` on the pipe fd. +- *Call resolution* (`resolve_calls` + `_resolve_with_pyright` `:181-380`) — opens the file via `textDocument/didOpen`, issues `textDocument/prepareCallHierarchy` per function entity, then `callHierarchy/outgoingCalls` per returned item. Edges are grouped by source byte range; multi-target ranges produce one `ambiguous` edge with the candidate list in `properties.candidates` (per ADR-028 confidence tiers, `:359-369`). Two AST-side enrichers — `_ambiguous_dict_dispatches` and `_dunder_call_dispatches` (`:1003-1145`) — fold dict-of-callables and `__call__`-on-instance patterns that pyright doesn't track natively into the same `grouped` map. Always followed by `textDocument/didClose` in `finally:` (`:380`). +- *Reference resolution* (`resolve_references` + `_resolve_references_with_pyright` `:228-453`) — hard cap of 2 000 sites per file (emits `CLA-PY-PY-REFERENCE-SITE-CAP` and returns early, `:238-250`); per-site `textDocument/references` queries with annotation-fallback retry (`:411-422`); deduplicates by `(from_id, to_id)` accumulator and finalises with `_reference_accumulator_to_edge` (`:922-937`). All exceptions are caught at the boundary and converted to fail-soft results. +- *AST function-indexing helpers* (`_build_function_index`, `_collect_entities`, `_CallSiteVisitor`, `_DictDispatchVisitor`, `_DunderCallDispatchVisitor` `:760-1145`) — a parallel AST pass independent from `extractor.py`'s walker; necessary because `PyrightSession` needs LSP positions (line/character) for every function and class plus the per-function call-site index, neither of which the wire shape carries. + +**Dependencies:** + +- Inbound: Rust core's plugin host (`crates/clarion-core/src/plugin/host.rs`) spawns this plugin via the `clarion-plugin-python` console script; the host's typed `protocol.rs` (`InitializeResult`, `AnalyzeFileResult`, `AnalyzeFileStats`, `ShutdownResult`) is the wire contract; the host's writer-actor (`clarion-storage`) consumes the emitted entities and edges; the `walking-skeleton` CI job invokes the full pipeline. +- Outbound: `pyright==1.1.409` (LSP server subprocess, pinned in both `pyproject.toml:20` and `plugin.toml:29`); `packaging>=24` (version-range parsing in the Wardline probe); Python stdlib only otherwise (`ast`, `json`, `subprocess`, `select`, `threading`, `importlib`, `pathlib`, `urllib.parse`). `wardline` is a **soft** outbound dependency — imported only to probe at `initialize`; absence is not an error. The doctrine asterisk noted in `docs/suite/loom.md` §5 is real: `wardline.core.registry` is imported by name (`wardline_probe.py:38`), and the manifest pins `[integrations.wardline] min_version=1.0.0 max_version=2.0.0` (`plugin.toml:48-55`). + +**Patterns Observed:** + +- **Protocol-typed wire boundary.** Every method handler returns a TypedDict whose shape mirrors the Rust host's serde structs exactly (`server.py:7-19` docstring enumerates this). The five JSON-RPC error codes used (`-32600`, `-32601`, `-32603`, `-32002`) are LSP-style (`server.py:51-54`). Out-of-spec frames raise `ProtocolError`, which propagates out of the loop and exits with status 1 (`server.py:284-285`). +- **Fail-soft pyright integration.** Every external failure mode of `pyright-langserver` (not installed, install-check rejection, init timeout, runtime timeout, transport-closed, broken pipe, OSError) is caught at the `resolve_calls` / `resolve_references` boundary, downgraded to a `CLA-PY-PYRIGHT-*` finding, and returned as "unresolved" counts in the result — never raised back into the dispatch loop (`pyright_session.py:202-217`, `265-280`). The 3-restart cap then disables the session entirely for the run. +- **Two-pass AST.** The extractor pass (`extractor.py`) produces wire entities + structural `contains` edges; a parallel AST pass inside `pyright_session.py` (`_build_function_index`, `_CallSiteVisitor`) builds the position-indexed function index pyright needs. The two never share a tree; this duplicates `ast.parse` work but keeps the extractor a pure function of source bytes. +- **`Protocol`-typed resolvers with No-Op fallback.** `CallResolver` and `ReferenceResolver` are `typing.Protocol`s with `NoOpCallResolver` / `NoOpReferenceResolver` defaults baked into `extractor.extract`'s kwargs (`extractor.py:83-84`, `247-249`). Tests can construct the extractor without spawning pyright. +- **Stdout-strictness via guard object.** `_GuardedTextStdout` raises rather than silently swallows; any library print() becomes a `StdoutGuardError`, which the dispatch boundary turns into a `_ERR_INTERNAL` JSON-RPC response (`server.py:259-260`). This is the plugin-side closure of WP2 UQ-WP2-08. +- **Path-jail-aware path handling.** `_resolve_module_path` relativises only the path used for the dotted qualname prefix; the wire `source.file_path` stays exactly as the host sent it, so the host's path-jail (which canonicalises against `project_root`) sees the original (`server.py:156-174`, `extractor.py:24-32`). +- **Single source of truth on ontology version.** The manifest declares `ontology_version = "0.5.0"` (`plugin.toml:46`); `server.py:36` redeclares the same constant `ONTOLOGY_VERSION = "0.5.0"`. Two declarations, no shared import — kept matched by hand per ADR-027. +- **B.8 fix layered defence.** The `@overload`-stub skip in `_has_overload_decorator` is the *fast path* for the named PEP 484 case; the same-id dedup loop in `_walk` is the *belt-and-suspenders* for anything the pattern-based check misses (aliased imports, `@singledispatch.register def _():`). Both feed the same wire-correctness invariant (no two entities with identical IDs) so the host's `UNIQUE(entities.id)` never trips mid-run (`extractor.py:283-294`, `624-637`, `645-652`). + +**Concerns:** + +- **Doctrine asterisk still live.** `wardline_probe.py:38` imports `wardline.core.registry` by name — exactly the Loom-doctrine asterisk called out in `docs/suite/loom.md` §5. Retirement condition is documented but not yet met. Not a defect; flagged because any architecture-quality review should know this is deliberate. +- **`ONTOLOGY_VERSION` is duplicated in two files (`server.py:36` and `plugin.toml:46`)** with no compile-time/runtime cross-check that they match. If a future ADR-027 minor bump updates one and forgets the other, the handshake validates the manifest value while the plugin behaves per the constant — silent skew. The comment at `server.py:38-41` acknowledges this and defers the manifest-flow-through. +- **`PyrightSession.close()` masks errors from the LSP `shutdown`/`exit` exchange** (`pyright_session.py:170`): timeouts, transport-closed, broken pipe, and `OSError` are all swallowed before the kill-and-wait. This is the correct behaviour at process-end, but it means a pyright that hangs on shutdown gives no signal beyond the eventual `process.kill()`. +- **`_resolve_with_pyright` busy-loops on mismatched `id` responses** (`pyright_session.py:663-666`). If pyright ever sends a stream of id-mismatched frames between request and response (server-initiated notifications, mismatched-cancel ack), the loop just keeps reading until the per-call deadline fires. The deadline upper-bounds it (5 s default), so this is bounded rather than fatal. +- **`_resolve_module_path`'s fall-through to the raw path on `ValueError`** (`server.py:170-173`) writes the absolute path into `source.file_path` of every emitted entity, which the host's path-jail check will reject. The comment says this is intentional ("fall back to the raw path so the host's logs show the drift"); whether that's the right failure mode versus an explicit per-file error finding is a design call worth noting for axiom-system-architect. +- **AST re-parse duplication.** `extractor.py` and `pyright_session._build_function_index` each call `ast.parse` on the same source bytes for every `analyze_file`. At elspeth-scale (~425k LOC Python) this is two AST walks per file, not one. Not yet measured; called out because the B.8 scale test on this branch is exactly where this would surface. + +**Confidence:** High — Read in full: `plugin.toml`, `pyproject.toml`, `server.py` (285), `extractor.py` (744), `qualname.py` (46), `wardline_probe.py` (56), `entity_id.py` (75), `stdout_guard.py` (62), `call_resolver.py` (64), `reference_resolver.py` (69), `__init__.py`, `__main__.py`. Sampled `pyright_session.py` top-level structure (every `def`/`class` declaration line) plus full reads of `__init__`, `close`, `resolve_calls`, `resolve_references`, `_resolve_with_pyright`, `_ensure_process`, `_record_restart_or_poison`, `_start_process`, `_initialize`, `_resolve_executable`, `_subprocess_env`, `_start_stderr_drain`, `_drain_stderr`, `_request`, `_notify`, `_live_process`, `_write_message`, `_read_message`. Cross-validated: B.8 `@overload` commit `29f0426` body cited verbatim, manifest pyright pin matches `pyproject.toml` pin (`1.1.409` in both `plugin.toml:29` and `pyproject.toml:20`), Wardline probe is initialize-only (single call site at `server.py:151`), the doctrine asterisk import path matches `loom.md` §5's wording. Tests directory inventory matches source-file inventory 1:1 (10 source files, 10 test files including `test_round_trip.py`). + +**Information Gaps:** + +- Did not exhaustively read `pyright_session.py` lines 715-1247 (the AST function-indexing helpers, dict-dispatch visitor, byte/position translators). Sampled enough to confirm shape but not every branch. +- Did not read the test files (`tests/test_*.py`); test coverage claims would require that step. +- Did not verify wire-shape claims by running the e2e script (`tests/e2e/sprint_1_walking_skeleton.sh`); compatibility is asserted from the Python TypedDicts vs. the Rust `protocol.rs` docstring at `server.py:7-19`, not from a live run on this branch. +- Did not chase `clarion-core/src/plugin/host.rs:132-154` to confirm the `RawEntity` / `RawSource` shape claim cited in `extractor.py:8-22`. Treated as authoritative because the extractor docstring is dated to the same commit family as the host. + +**Caveats:** + +- LOC counts via `wc -l` include blank lines and docstring lines. The "actual code" share is lower; `extractor.py:1-54` is all docstring, for instance. +- "B.8 +98 lines on this branch" is taken from the discovery-findings document's framing; I did not run `git diff main...HEAD -- extractor.py | wc -l` to verify exactness, but the commit `29f0426` body matches the behaviour read in `extractor.py:567-668`. +- The `wardline_probe` integration is described as "fail-soft" based on the three return shapes; whether downstream consult-mode briefings actually do anything different when `status == "enabled"` versus `"absent"` is out of scope for this entry (it would require reading the MCP briefing assembler). + +**Risk Assessment:** + +- *Doctrine asterisk surface.* The `wardline.core.registry` import (`wardline_probe.py:38`) is a known, ratified asterisk under `loom.md` §5 — risk is bounded by the documented retirement condition, but it remains a point where the federation axiom is consciously bent. Any review must surface it. +- *Wire-shape skew risk.* The plugin re-declares `ONTOLOGY_VERSION = "0.5.0"` (`server.py:36`) and `entity_kinds`/`edge_kinds`/`rule_id_prefix` (`plugin.toml:35-39`) as parallel sources of truth with the host's `protocol.rs`. Skew here would surface only at the handshake — the host's validator rejects mismatched `ontology_version` per ADR-027, so the risk is detected, not silent. +- *Pyright-availability dependency.* The walking-skeleton CI job and any `analyze` run that requests `calls` or `references` edges hard-depends on `pyright-langserver` resolvable via PATH, the active venv, or absolute path (`pyright_session.py:618-625`). On hosts without Node, the plugin still ships entities (the no-op fallback path), but every function emits as "unresolved" — observable but not catastrophic. +- *B.8 scale-test risk.* This branch (`sprint-2/b8-scale-test`) is precisely the change that hardens the extractor against the failure mode it was discovered under (UNIQUE collision on `@overload` stubs at elspeth scale). The fix is layered (semantic skip + safety-net dedup); the residual risk is aliased-overload imports plus identical-qualname intentional redefinitions, both of which now hit the safety-net path and log to stderr rather than crash. diff --git a/docs/arch-analysis-2026-05-18-1244/03-diagrams.md b/docs/arch-analysis-2026-05-18-1244/03-diagrams.md new file mode 100644 index 00000000..181d5681 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/03-diagrams.md @@ -0,0 +1,281 @@ +# 03 — Architecture Diagrams + +**Repository:** `/home/john/clarion` +**Branch:** `sprint-2/b8-scale-test` +**Generated:** 2026-05-18 + +All diagrams are Mermaid, validated through the Mermaid Live renderer. They draw from `01-discovery-findings.md` and `02-subsystem-catalog.md`. + +Five views, in the C4-inspired order — context, container, then two narrative sequences and one component zoom. + +--- + +## 1 — System Context (C4 L1): Clarion in the Loom federation + +Clarion-as-a-system, the actors and the external systems it talks to. The two solid blue siblings (Filigree, Wardline) are owned by the same author and explicitly enrich-only / soft-import per `docs/suite/loom.md` §3–§5. The dashed line to Wardline marks the named v0.1 doctrine asterisk. + +```mermaid +flowchart LR + classDef person fill:#1168bd,color:#fff,stroke:#0b4884 + classDef softwareSystem fill:#1168bd,color:#fff,stroke:#0b4884 + classDef external fill:#999999,color:#fff,stroke:#666666 + classDef sibling fill:#438dd5,color:#fff,stroke:#2e6295 + + OP["Operator
(developer / CI)"]:::person + AGENT["Consult-mode LLM agent
(via MCP client)"]:::person + + CLARION["Clarion
Code-archaeology service
Rust core + language plugins
SQLite-backed local state"]:::softwareSystem + + PYRIGHT["pyright-langserver
(LSP subprocess)"]:::external + OPENROUTER["OpenRouter HTTP API
(LLM provider)"]:::external + + FILIGREE["Filigree
Issue tracker
(Loom sibling — enrich only)"]:::sibling + WARDLINE["Wardline
Static checks + fingerprints
(Loom sibling — soft import)"]:::sibling + + SOURCE[("Source tree
(project_root)")] + + OP -->|"clarion install / analyze / serve"| CLARION + AGENT -->|"MCP stdio
2025-11-25"| CLARION + CLARION -->|"reads project files
under jail"| SOURCE + CLARION -->|"spawns LSP subprocess
(per Python plugin)"| PYRIGHT + CLARION -->|"HTTPS chat/completions
strict-JSON, budget-bounded"| OPENROUTER + CLARION -->|"GET /api/entity-associations
(enrich-only)"| FILIGREE + CLARION -.->|"import probe at handshake
(asterisk: loom.md §5)"| WARDLINE +``` + +**Key facts:** +- One operator + one MCP client are the primary actors. +- Two outbound HTTP integrations (OpenRouter, Filigree) plus one subprocess (pyright). Wardline is import-only. +- The MCP wire is stdio, not HTTP — `clarion serve` runs in the foreground of the agent's process tree. + +--- + +## 2 — Container view (C4 L2): inside the binary + +The `clarion` binary is the only deployment artifact. Five workspace crates inside it; two subprocess-protocol peers (one real Python plugin, one test fixture); three external endpoints; two persistent files under `.clarion/`. + +```mermaid +flowchart TB + classDef binary fill:#1168bd,color:#fff,stroke:#0b4884 + classDef crate fill:#85bbf0,color:#000,stroke:#5d82a8 + classDef subproc fill:#fff2cc,color:#000,stroke:#d6b656 + classDef datastore fill:#cccccc,color:#000,stroke:#666 + classDef external fill:#999999,color:#fff,stroke:#666 + + subgraph CLARION_HOST["clarion binary (single executable)"] + direction TB + CLI["clarion-cli
install / analyze / serve"]:::binary + CORE["clarion-core
entity-ID + PluginHost
LlmProvider + manifest
jail / limits / breaker"]:::crate + STORAGE["clarion-storage
writer-actor (sole rusqlite)
deadpool reader pool
9 WriterCmd variants"]:::crate + MCP["clarion-mcp
MCP 2025-11-25
7 read tools
5-tuple cache + budget"]:::crate + end + + PYPLUGIN["plugins/python
clarion-plugin-python
JSON-RPC subprocess"]:::subproc + FIXTURE["clarion-plugin-fixture
(test-only)"]:::subproc + + PYRIGHT["pyright-langserver"]:::external + OPENROUTER["OpenRouter HTTP"]:::external + FILIGREE_HTTP["Filigree HTTP"]:::external + + DB[(".clarion/clarion.db
SQLite WAL")]:::datastore + YAML[(".clarion/clarion.yaml
operator config")]:::datastore + + AGENT["LLM agent (MCP client)"] + OP["Operator (shell / CI)"] + + OP -->|"argv"| CLI + AGENT -->|"stdio JSON-RPC"| CLI + CLI --> CORE + CLI --> STORAGE + CLI --> MCP + MCP --> CORE + MCP --> STORAGE + STORAGE --> CORE + CLI -->|"discover + spawn"| PYPLUGIN + CLI -.->|"spawn (tests only)"| FIXTURE + PYPLUGIN -->|"spawns once
per session"| PYRIGHT + MCP -->|"strict-JSON"| OPENROUTER + MCP -->|"GET enrich"| FILIGREE_HTTP + STORAGE -->|"writer + readers"| DB + CLI -->|"writes on install"| DB + CLI -->|"reads on serve"| YAML +``` + +**Things worth noting:** +- The Rust crate graph is acyclic: `cli` → {`mcp`, `storage`, `core`}; `mcp` → {`storage`, `core`}; `storage` → `core` (one symbol, `EdgeConfidence`). +- The Python plugin is *not* a Rust crate; the only "dep" is the host-spawn-subprocess contract. +- The MCP server speaks a separate stdio session from the analyze run. They can be running concurrently against the same `.clarion/clarion.db`; correctness relies entirely on `clarion-storage`'s WAL + `busy_timeout=5000` pragma discipline. + +--- + +## 3 — `clarion analyze` run (sequence) + +The happy path and the two named failure modes (`SoftFailed`, `HardFailed`). The `RunOutcome` taxonomy is at `crates/clarion-cli/src/analyze.rs:558–563`; the three terminal branches differ by *which* `WriterCmd` they send. + +```mermaid +sequenceDiagram + autonumber + participant OP as Operator + participant CLI as clarion-cli
analyze::run + participant CORE as clarion-core
PluginHost + participant PLUGIN as Plugin subprocess
(Python or fixture) + participant WRITER as clarion-storage
writer-actor + participant DB as .clarion/clarion.db + + OP->>CLI: clarion analyze [PATH] + CLI->>WRITER: Writer::spawn(db_path) + CLI->>WRITER: BeginRun(run_id) + WRITER->>DB: INSERT runs (status=running) + BEGIN + Note over CLI: discover plugins on $PATH
(clarion-plugin-*) + CLI->>CORE: discover() + loop per plugin + CLI->>CORE: PluginHost::spawn (pre_exec setrlimit) + CORE->>PLUGIN: stdin/stdout pipes + CORE->>PLUGIN: initialize (handshake) + PLUGIN-->>CORE: InitializeResult + capabilities + CORE->>PLUGIN: initialized + loop per file in plugin extensions + CLI->>CORE: host.analyze_file(path) + CORE->>PLUGIN: analyze_file + PLUGIN-->>CORE: entities + edges + stats + Note over CORE: 5-step validator pipeline
field-size / kind / id / jail / cap + CORE-->>CLI: AcceptedEntity/Edge + HostFinding + end + CLI->>WRITER: InsertEntity * N + CLI->>WRITER: ReplaceUnresolvedCallSitesForCaller * N + CLI->>WRITER: InsertEdge * N (enforce_edge_contract) + WRITER->>DB: batched INSERTs (cadence=50) + CLI->>CORE: host.shutdown / kill / reap + end + alt all plugins OK + CLI->>WRITER: CommitRun(Completed, stats_json) + WRITER->>DB: UPDATE runs SET status='completed' + COMMIT + else some plugin crashed (SoftFailed) + CLI->>WRITER: CommitRun(Failed, failure_reason) + WRITER->>DB: UPDATE runs SET status='failed' + COMMIT (partial work kept) + else writer error (HardFailed) + CLI->>WRITER: FailRun(reason) + WRITER->>DB: ROLLBACK + UPDATE runs SET status='failed' + end + CLI-->>OP: exit code (0 / nonzero) +``` + +**Key invariants:** +- All writes funnel through a single writer-actor task that owns the sole `rusqlite::Connection` (ADR-011). +- The five-step host validator pipeline is the place where plugin-side guarantees become host-side facts: field-size, kind-declared, entity-id-matches, path-jail, entity-cap. Steps 0–2 only drop offending records; steps 3–4 escalate to plugin termination on breaker trip. +- The `SoftFailed` branch is the one path where the same SQLite transaction carries both accepted entities *and* a `UPDATE runs SET status='failed'` — a partial-work-with-marker invariant. + +--- + +## 4 — MCP `summary` tool with cache miss → LLM dispatch (sequence) + +The richest narrative path in the codebase: the ADR-007 5-tuple cache lookup, budget reservation, `spawn_blocking` to the synchronous `LlmProvider`, JSON-shape validation, and writeback via the writer-actor. + +```mermaid +sequenceDiagram + autonumber + participant AGENT as MCP client
(LLM agent) + participant MCP as clarion-mcp
tool_summary + participant READER as clarion-storage
ReaderPool + participant CACHE as summary_cache
(SQLite) + participant BUDGET as BudgetLedger
(in-memory) + participant PROV as OpenRouter
(LlmProvider) + participant WRITER as writer-actor + + AGENT->>MCP: tools/call summary { id } + MCP->>READER: with_reader → entity_by_id + summary_cache_lookup + READER->>CACHE: SELECT by 5-tuple
(entity_id, content_hash, prompt_template_id,
model_tier, guidance_fingerprint) + alt cache hit and not stale and not expired + CACHE-->>MCP: SummaryCacheEntry + MCP->>WRITER: TouchSummaryCache(last_accessed_at) + MCP-->>AGENT: summary envelope (cached=true) + else cache miss / stale_semantic / >180 days + MCP->>BUDGET: reserve_budget (pessimistic token estimate) + alt budget exhausted + BUDGET-->>MCP: token-ceiling-exceeded (sticky) + MCP-->>AGENT: ok=false, retryable=false + else budget OK + BUDGET-->>MCP: BudgetReservation (RAII) + Note over MCP: build_leaf_summary_prompt
(LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1") + MCP->>PROV: spawn_blocking → invoke(LlmRequest)
response_format strict-JSON + PROV-->>MCP: LlmResponse (text + usage) + MCP->>BUDGET: commit(usage.input + output) + MCP->>WRITER: UpsertSummaryCache(SummaryCacheKey, payload) + WRITER-->>MCP: ack via oneshot + MCP-->>AGENT: summary envelope (cached=false) + end + end +``` + +**Notes that don't fit on the diagram:** +- The 4-tuple `InferredEdgeCacheKey` for the inferred-edges path is structurally identical: `(caller_entity_id, caller_content_hash, model_id, prompt_version)`. The flow looks the same except for an additional **in-flight coalescer** (`inferred_inflight: HashMap`) with a 60-second timeout so concurrent identical dispatches share one LLM call. +- `BudgetLedger.blocked` is sticky for the lifetime of `ServerState` — once one reservation overshoots, every subsequent LLM tool returns `token-ceiling-exceeded` until process restart. No reset path. +- Filigree's `issues_for` path *also* uses `spawn_blocking` (for `reqwest::blocking`) — same bridging shape, no cache, three independent skip paths route to `issues_unavailable` to honour Loom's enrich-only contract. + +--- + +## 5 — Component zoom: `clarion-core::plugin::host` validator pipeline + +The internal organisation of `PluginHost::analyze_file` — the per-file dispatch shape inside the plugin host supervisor. Sourced from `crates/clarion-core/src/plugin/host.rs:1031–1198`. + +```mermaid +flowchart TB + classDef accept fill:#c9e7c9,color:#000,stroke:#5a8a5a + classDef drop fill:#fff2cc,color:#000,stroke:#d6b656 + classDef kill fill:#f4cccc,color:#000,stroke:#a64d4d + classDef entry fill:#85bbf0,color:#000,stroke:#5d82a8 + + START["host.analyze_file(path)"]:::entry + SEND["Send analyze_file request
over JSON-RPC + read frame"]:::entry + OUTCOME["Decoded AnalyzeFileOutcome:
entities, edges, stats"]:::entry + + S0{"0. field-size cap
(4 KiB scalar, 64 KiB extra)"} + S1{"1. ontology declared-kind
(manifest entity_kinds)"} + S2{"2. entity-id identity
(canonical_qualified_name ≡ id)"} + S3{"3. path-jail check
+ PathEscapeBreaker tick"} + S4{"4. entity-cap check
(plugin-declared budget)"} + + EDGES["process_edges
(drop-only, no kill paths)"] + STATS["process_stats
(record p95 latency)"] + OUT_ACCEPT["AcceptedEntity ⇒ caller"]:::accept + DROP_F["drop record
+ HostFinding"]:::drop + KILL_J["kill plugin
(disabled-path-escape)"]:::kill + KILL_C["kill plugin
(entity-cap exceeded)"]:::kill + + START --> SEND --> OUTCOME --> S0 + S0 -->|"oversize"| DROP_F + S0 -->|"OK"| S1 + S1 -->|"undeclared kind"| DROP_F + S1 -->|"OK"| S2 + S2 -->|"mismatch"| DROP_F + S2 -->|"OK"| S3 + S3 -->|"escape + breaker tripped"| KILL_J + S3 -->|"escape (under threshold)"| DROP_F + S3 -->|"OK"| S4 + S4 -->|"exceeded"| KILL_C + S4 -->|"OK"| OUT_ACCEPT + OUTCOME --> EDGES + OUTCOME --> STATS +``` + +**Design notes:** +- Steps 0–2 are **pure-function validators** (`oversize_field`, `oversize_edge_field`, `invalid_unresolved_call_site_reason`, `validate_kind_string`); they emit a `HostFinding` and drop the offending row. +- Steps 3–4 carry **kill paths** because they involve cross-record state: `PathEscapeBreaker` ticks once per offending entity and trips after a documented threshold, and entity-cap is a per-plugin budget that's only meaningful in aggregate. +- The same drop-on-violation discipline is applied to edges, but with **no kill paths** — edges do not participate in breakers. Trade-off: an edge-heavy file can spam many findings; an entity-heavy file is bounded by the cap. + +--- + +## Coverage notes + +| C4 level | Diagram | Subsystems covered | +|----------|---------|---------------------| +| L1 Context | #1 | Clarion as a whole, all 5 external dependencies | +| L2 Container | #2 | All 6 internal subsystems + 5 external | +| L3 Component | #5 | `clarion-core::plugin::host` (largest production file) | +| Sequence | #3 | `clarion analyze` lifecycle, all 3 terminal branches | +| Sequence | #4 | MCP `summary` LLM dispatch, ADR-007 5-tuple cache | + +What's deliberately not drawn here (size / clarity vs. info-value tradeoff): +- A component view of `clarion-mcp::lib.rs` — it has a clean banded structure (protocol surface → `ServerState` → per-tool handlers → LLM pipelines → transport loop → helpers) but the 7 tools × 4 substates each would dominate a single diagram. The catalog entry's tool table is the substitute. +- A component view of `clarion-storage::writer` — the 9 `WriterCmd` variants are clean and listed in the catalog; visualising the per-variant SQL would obscure rather than illuminate. +- A schema ER diagram — the catalog's ASCII schema sketch is sufficient for v0.1's 8-table footprint. diff --git a/docs/arch-analysis-2026-05-18-1244/04-final-report.md b/docs/arch-analysis-2026-05-18-1244/04-final-report.md new file mode 100644 index 00000000..5af69cce --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/04-final-report.md @@ -0,0 +1,270 @@ +# Clarion — Architecture Analysis Report + +**Repository:** `/home/john/clarion` +**Branch:** `sprint-2/b8-scale-test` (17 commits ahead of `main`) +**Commit at validation:** `363bb0a` (working-tree refreshed during validation pass) +**Tags:** `v0.1-sprint-1`, `v0.1-sprint-2` +**Date:** 2026-05-18 +**Methodology:** `axiom-system-archaeologist:analyze-codebase` — coordinator + per-subsystem subagents + validation gates +**Source artifacts:** +- `01-discovery-findings.md` — holistic scan, 384 lines +- `02-subsystem-catalog.md` — six subsystem entries, ~650 lines, validation **NEEDS_REVISION (warnings)** → corrections applied inline +- `03-diagrams.md` — five Mermaid diagrams (C4 Context + Container + 2 sequences + 1 component), validation **APPROVED** + +--- + +## 1. Executive summary + +Clarion is a **code-archaeology service** — single-binary Rust core + out-of-process language plugins — that ingests a Python codebase, normalises it into a typed entity/edge graph in local SQLite, and serves that graph plus on-demand LLM-generated leaf summaries and inferred call edges to consult-mode LLM agents over MCP. It is one of four products in the Loom suite (Filigree, Wardline, Clarion, Shuttle) authored by a single owner; the federation axiom (solo-useful + pairwise-composable + enrich-only, `docs/suite/loom.md` §3–§5) is the load-bearing constraint on cross-product design. + +The codebase is **roughly 30 000 LOC** — 24 727 Rust across 5 workspace crates, 5 629 Python in one plugin — backed by 92 markdown documents (requirements / system design / detailed design / 25 Accepted ADRs / per-sprint work-package docs / sprint sign-offs / handoff memos). Sprint 1 closed with the walking-skeleton end-to-end at `v0.1-sprint-1`; Sprint 2 closed at `v0.1-sprint-2` with seven MCP tools live and the B.8 scale test green against the `elspeth` corpus after a repair rerun. The current branch carries the B.8 fix follow-up (an extractor dedup hardening and an `ADR-031` schema-validation policy that adds `CHECK` constraints to closed core-owned vocabularies). + +**Architectural shape.** A clean layered crate graph (acyclic) — `clarion-core` (entity-ID, plugin host, LLM provider abstraction) → `clarion-storage` (writer-actor + reader-pool over a single SQLite database) → `clarion-mcp` (MCP server, ADR-007 5-tuple cache, budget ledger) → `clarion-cli` (glue binary). The Python plugin is a separate process speaking JSON-RPC over Content-Length-framed stdio. Two named v0.1 federation asterisks (Wardline→Filigree pipeline coupling routed through Clarion; Python plugin's soft import of `wardline.core.registry`) are documented and have retirement conditions. + +**Standout strengths.** +- **Boundary discipline is real, not aspirational.** Plugin authority is enforced at the host (5-step validator pipeline at `clarion-core/src/plugin/host.rs:1031–1198`); storage authority is enforced at the writer-actor (edge contract with three `CLA-INFRA-EDGE-*` codes at `writer.rs:411`); cache-key correctness is enforced at the call site (ADR-007 5-tuple at `clarion-mcp/src/lib.rs:1010–1016`). Defence-in-depth between the writer-actor and ADR-031's new SQL `CHECK` clauses is a thoughtful choice, not a copy of one to the other. +- **Plugin separation is a process boundary, not a trait abstraction.** The wire protocol is the contract; the test fixture is a 131-LOC second implementation that proves the contract by speaking it. +- **Sprint-1 lock-ins held under Sprint-2 pressure.** L1–L9 from `docs/implementation/sprint-1/README.md` §4 are visible as concrete code shapes: ADR-003 entity-ID parity, ADR-011 actor/pool split, ADR-021 jail+limits, ADR-022 ontology authority, all still visibly load-bearing in Sprint-2 code without rewriting. +- **No god-files.** The two largest source files (`clarion-core/src/plugin/host.rs` at 3 126 LOC and `clarion-mcp/src/lib.rs` at 2 712 LOC, growing during Sprint-2 follow-up) are coherent, banded, and internally documented. The catalog confirms `host.rs` is roughly 1 450 production LOC plus 1 700 LOC of test scaffolding. + +**Notable risks (full list in §5).** +- One single-file `analyze::run` of ~500 lines orchestrates the analyze lifecycle without coverage for its `SoftFailed` branch (the soft-fail path that commits partial entity work and a `runs.status='failed'` UPDATE inside the same transaction). +- Two source-of-truth duplications without compile-time enforcement: edge ontology (writer, manifest, ADR) and Python plugin `ONTOLOGY_VERSION` (`server.py` + `plugin.toml`). +- One MCP raw SQL site (`reference_neighbors` at `clarion-mcp/src/lib.rs:2381`) bypasses the storage layer's typed query helpers and would not be caught by storage-side schema tests. +- ADR-024's single edit-in-place migration has been edited three times; the retirement trigger ("external operator builds `.clarion/clarion.db` from a published Clarion build") is documented in-file but is on manual discipline only. +- `BudgetLedger.blocked` is sticky for the lifetime of `ServerState` — one ceiling breach disables LLM tools until process restart, with no documented reset path. + +**Recommended next steps (full list in §7).** +- Add `SoftFailed`-branch integration coverage to `crates/clarion-cli/tests/analyze.rs` before any extraction refactor of `analyze::run`. +- Extract the per-tool dispatch handlers from `clarion-mcp/src/lib.rs` into a sibling `tools/` submodule once a Sprint-3 surface settles. +- Audit cross-product vocabulary duplications: one issue per duplication (edge ontology; Python `ONTOLOGY_VERSION`). +- Surface a Filigree-Linked tracker entry for the ADR-024 migration-retirement trigger so the manual condition is observable. + +--- + +## 2. Architecture at a glance + +Clarion's deployment model is **single binary + one subprocess per language plugin**. Operators run `clarion install` once to lay down `.clarion/clarion.db` + `.clarion/clarion.yaml` + a `.gitignore`. Then `clarion analyze` does the ingest run, and `clarion serve` (Sprint-2 addition) hosts the MCP stdio server for consult-mode agents. The plugin host spawns each `clarion-plugin-*` binary discovered on `$PATH`, speaks five JSON-RPC methods (`initialize` / `initialized` / `analyze_file` / `shutdown` / `exit`), and validates everything coming back through the five-step pipeline before persisting via the writer-actor. + +The federation context, the binary's container view, the analyze lifecycle, the MCP `summary` cache-miss → LLM dispatch flow, and the plugin host validator pipeline are diagrammed in `03-diagrams.md`. They are not duplicated here — refer to that file for the visual reference. + +| Layer | Crate(s) | Production LOC | Owns | +|---|---|---|---| +| Domain + safety | `clarion-core` | ~3 100 | EntityId grammar; PluginHost supervisor; LlmProvider trait + OpenRouter; manifest parser; jail + RSS + entity + crash-loop breaker | +| Persistence | `clarion-storage` | ~1 950 | Writer-actor (sole `rusqlite::Connection`); deadpool-sqlite reader pool; schema migration runner; PRAGMA discipline; edge-contract validator; 5-tuple summary cache + 4-tuple inferred-edge cache | +| Read surface | `clarion-mcp` | ~3 300 (`lib.rs` 2 712) | MCP 2025-11-25 over stdio; 7 read tools; ADR-007 cache lookup; budget ledger; in-flight LLM dispatch coalescer; Filigree enrich-only HTTP client | +| Glue + UX | `clarion-cli` | ~1 740 | `clap` dispatch; `.clarion/` bootstrap; analyze orchestrator (~500-line async run); MCP server wiring | +| Test fixture | `clarion-plugin-fixture` | 131 | Protocol-compatible test stand-in for the host's `host_subprocess` integration test | +| Language plugin | `plugins/python` | ~2 670 | Python AST → entities + edges; `pyright-langserver` LSP client (1 251 LOC); Wardline soft-import probe; ADR-018 canonical qualname | + +The Rust workspace lints at `unsafe_code = "deny"` (downgraded from `forbid` with one documented exception: `pre_exec` + `setrlimit` in `clarion-core/src/plugin/limits.rs`, the only `unsafe` block in the codebase). Clippy is `pedantic = warn` with three pragmatic allows. Python is `mypy --strict`, `ruff select = ["ALL"]` with pragmatic ignores, complexity capped at 15 to match clippy. ADR-023 names these and the corresponding CI jobs as the floor; every PR must pass them. + +--- + +## 3. Subsystem walkthrough + +Each entry below is a 1–2 paragraph synthesis of the corresponding catalog entry. For the full per-subsystem treatment with file:line citations, see `02-subsystem-catalog.md`. + +### 3.1 `clarion-core` — domain + safety + +`clarion-core` owns the four primitives every other crate depends on: the canonical `EntityId` (a three-segment newtype validated against the cross-language `fixtures/entity_id.json` parity proof); the plugin host (`PluginHost` — generic over reader/writer so subprocess and in-process mock share one validator pipeline); the `LlmProvider` trait with `OpenRouterProvider` + `RecordingProvider` implementations and stable prompt-template IDs (`LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1"`, `INFERRED_CALLS_PROMPT_VERSION = "inferred-calls-v1"` at `llm_provider.rs:10–11`); and the safety ceilings (jail, content-length, entity cap, RSS via `setrlimit`, crash-loop breaker). + +The crate's two heavy files are coherent: `plugin/host.rs` (3 126 LOC) is one struct + two constructors + a five-step validator pipeline + a 1 700-LOC test suite; `llm_provider.rs` (948 LOC) is request/response DTOs + the trait + `RecordingProvider` + `OpenRouterProvider` with its strict-JSON schema gate (the B.8 GREEN-rerun fix at `response_format_for_purpose:297`). Caching is not done in `clarion-core` — the 5-tuple cache key is materialised inside `clarion-mcp` and `clarion-storage`; the provider is a stateless dispatcher. The crate is fully synchronous (no `tokio` dependency); MCP-side async-from-sync bridging is via `spawn_blocking`. + +### 3.2 `clarion-storage` — persistence + +A writer-actor (single `tokio::task` owning the sole `rusqlite::Connection`) plus a `deadpool-sqlite` reader pool, both targeting one `.clarion/clarion.db` file. Nine `WriterCmd` variants (`BeginRun` / `InsertEntity` / `InsertEdge` / `InsertInferredEdges` / `UpsertSummaryCache` / `TouchSummaryCache` / `ReplaceUnresolvedCallSitesForCaller` / `CommitRun` / `FailRun`), each with a typed `oneshot` ack. Batch cadence is 50 writes (`DEFAULT_BATCH_SIZE` at `writer.rs:35`); query-time MCP writes interleave with analyze-time runs via `query_time_write` which commits the open batch before reopening `BEGIN` if a run is in progress. + +The schema is a single migration (289 lines at `migrations/0001_initial_schema.sql`) covering 8 base tables, 1 FTS5 virtual, 3 triggers, 1 view, 2 generated columns. ADR-031 (new on this branch) adds `CHECK` constraints on closed core-owned vocabularies (`edges.confidence`, `findings.{kind,severity,status}`, `summary_cache.stale_semantic`, `runs.status`) and deliberately omits them from plugin-extensible columns (`entities.kind`, `edges.kind`) — the writer-actor remains the canonical validator; CHECK is defence-in-depth. The migration has been edited three times (initial; 2026-05-03 ADR-024 vocabulary rename; 2026-05-18 ADR-031 CHECKs) under ADR-024's "edit-in-place until external operators build from a published Clarion build" policy. + +### 3.3 `clarion-mcp` — read surface + +The Sprint-2 addition. One Rust crate, three source files (`lib.rs` 2 712 + `config.rs` 352 + `filigree.rs` 238) plus a 1 710-line integration test file. The `lib.rs` grew through B.8 follow-up commits (`87036b1` reservation-poison fix; `363bb0a` inferred-target pre-filter) — visible growth trajectory, monitored not refactor-blocked. Speaks MCP protocol revision `2025-11-25` over stdio. Seven read tools (`entity_at`, `find_entity`, `callers_of`, `execution_paths_from`, `summary`, `issues_for`, `neighborhood`). Six are thin dispatch over `clarion-storage` helpers; the seventh (`summary`) plus the `confidence=inferred` branches of three others carry substantive LLM logic — cache lookup (ADR-007 5-tuple summary, 4-tuple inferred), budget reservation with RAII rollback, in-flight dispatch coalescing via a `broadcast` channel with a 60-second timeout, prompt construction via `clarion-core` helpers, provider invocation on `spawn_blocking`, JSON-shape validation, writeback via the writer-actor. + +Filigree integration is genuinely enrich-only: three independent skip paths route to an `issues_unavailable` envelope (`filigree-disabled` / `filigree-unreachable` / `filigree-client-error` / `entity-not-found`). The other six tools have no Filigree dependency. The single architectural smell is one raw SQL site (`reference_neighbors` at `lib.rs:2381`) that bypasses the storage layer; everything else routes through typed query helpers. + +### 3.4 `clarion-cli` — glue binary + +The `clarion` binary; `clap`-driven three-subcommand dispatch (`install`, `analyze`, `serve`). Loads `.env` from CWD or ancestor before tracing init. `install.rs` (168 LOC) is the only place that opens SQLite directly — apply PRAGMAs + migrations, write a stub `config.json`, write the ADR-005 `.gitignore`, write the operator `clarion.yaml`. `serve.rs` (136 LOC) wires a single-thread current-thread Tokio runtime, an LLM-only `Writer`, a `ReaderPool` (size 16), and the MCP server. + +The orchestrator is `analyze.rs` (1 436 LOC) with `analyze::run` a single ~500-line async function marked `#[allow(clippy::too_many_lines)]`. It owns plugin discovery, source-tree walk, per-plugin `spawn_blocking` dispatch, crash-loop accounting via the breaker from `clarion-core`, and the three-way `RunOutcome` resolution (`Completed` → `CommitRun(Completed)`; `SoftFailed` → `CommitRun(Failed)` with partial work persisted; `HardFailed` → `FailRun` rolling everything back). The phase banners inside `analyze::run` mark the obvious seams; extraction is a worthwhile but currently un-test-covered refactor (see §5). + +### 3.5 `clarion-plugin-fixture` — protocol test stand-in + +131 LOC across `main.rs` + `lib.rs`. Speaks the same Content-Length-framed JSON-RPC 2.0 protocol as a real plugin, but with hard-coded responses (one stub entity, no edges, fixed `ontology_version = "0.1.0"`). Consumed only by `crates/clarion-core/tests/host_subprocess.rs`. Re-uses `clarion-core`'s typed protocol structs so a breaking change to the wire shape fails compilation rather than at runtime. Same `ContentLengthCeiling::DEFAULT` (8 MiB) as production plugins. + +### 3.6 `plugins/python` — Python language plugin + +Ten Python files, 2 670 LOC. Speaks the L4 JSON-RPC protocol; uses `pyright-langserver` (pinned to `1.1.409`) for cross-reference resolution. The largest file is `pyright_session.py` at 1 251 LOC — a long-running LSP client with three-restart-then-poison fail-soft semantics, a 5-second per-call deadline, and a 64 KiB stderr-tail ring buffer for diagnostics. `extractor.py` (744 LOC, +98 on this branch for the B.8 fix) is the AST → wire-shape pass; the B.8 fix is layered defence — a semantic skip for `@overload` stubs plus a first-wins safety-net dedup that also catches aliased overload imports and `@singledispatch.register def _():`. + +`wardline_probe.py` runs once per session at handshake. The `wardline.core.registry` import (`wardline_probe.py:38`) is the named v0.1 doctrine asterisk — Sprint 1 only proves the import + version pin; consumption is deferred. `ONTOLOGY_VERSION = "0.5.0"` is declared in both `plugin.toml:46` and `server.py:36` without a cross-check; the handshake validates the manifest value, leaving the constant as a maintenance hazard. + +--- + +## 4. Cross-cutting concerns + +The following spans more than one subsystem and is governed by either an ADR or by `docs/suite/loom.md`. All are visible in catalog citations. + +| Concern | Governance | Implementation sites | +|---|---|---| +| **Entity-ID format** (3 colon-segments) | ADR-003 + ADR-022 | `clarion-core::entity_id.rs` (Rust); `plugins/python/.../entity_id.py` (Python); `fixtures/entity_id.json` (parity proof) | +| **JSON-RPC L4 protocol** (Content-Length framing, 5 methods, 8 MiB cap) | ADR-002 | `clarion-core::plugin::transport` + `protocol.rs`; `clarion-plugin-fixture::main`; `plugins/python/.../server.py` | +| **Plugin authority + jail + RSS** | ADR-021 | `clarion-core::plugin::{jail, limits, breaker, host}` | +| **Core / plugin ontology ownership** | ADR-022 | Host validator pipeline + manifest validator | +| **Edge confidence tiers** (`resolved` / `ambiguous` / `inferred`) | ADR-028 | `clarion-storage::writer::enforce_edge_contract`; `clarion-mcp::optional_confidence` | +| **Edge ontology** (`contains` / `calls` / `references` + 6 anchored / structural kinds) | ADR-026 / ADR-028 | Hard-coded in `clarion-storage::writer.rs:394–401`; declared in `plugin.toml:38`; documented in ADR — **3-place duplication, no cross-check** | +| **Ontology version semver** (currently `0.5.0` after B.5*) | ADR-027 | Validated at host handshake; declared in `plugin.toml:46` + `server.py:36` | +| **Summary cache 5-tuple key** | ADR-007 | `clarion-storage::cache::SummaryCacheKey`; lookup in `clarion-mcp::read_summary_inputs:1010–1016` | +| **Schema migration governance** (edit-in-place until external build) | ADR-024 | `migrations/0001_initial_schema.sql` + `schema.rs`; manual retirement trigger | +| **Schema-validation policy** (CHECK on closed vocabularies, not on plugin-extensible) | ADR-031 (new) | Six CHECK clauses in the migration; writer-actor remains canonical validator | +| **Loom federation axiom** (solo-useful + pairwise-composable + enrich-only) | `docs/suite/loom.md` §3–§5 | `clarion-mcp::filigree` (enrich-only); `plugins/python/.../wardline_probe.py` (soft import; the named asterisk) | +| **Filigree entity bindings** | ADR-029 | `clarion-mcp::filigree::EntityAssociation` + `FiligreeLookup`; `IssuesForAccumulator` drift classifier | +| **Summary scope (leaf-only for v0.1)** | ADR-030 | `LEAF_SUMMARY_PROMPT_TEMPLATE_ID` is the single template; `summary` tool description encodes leaf scope | +| **Tooling baseline** (cargo fmt / clippy -D warnings / nextest / doc-D / deny; ruff / mypy / pytest) | ADR-023 | `.github/workflows/ci.yml`: three jobs (`rust`, `python-plugin`, `walking-skeleton`) | + +--- + +## 5. Observations & risks (synthesised) + +This section folds the per-subsystem "Concerns" sections of the catalog into a prioritised global view. Each entry cites the originating catalog entry (and source line numbers where they sharpen the claim). + +### 5.1 High — worth a Sprint-3 thread + +**H-1. `analyze::run` is a single ~500-line `async fn` whose `SoftFailed` branch has no end-to-end coverage.** +Catalog: `clarion-cli` §Concerns. Source: `crates/clarion-cli/src/analyze.rs:40–542` is the function; `:421–429` is the `Completed` → `SoftFailed` promotion (`Completed` + non-empty `crash_reasons`); `:478–509` is the `SoftFailed` branch that folds `UPDATE runs SET status='failed'` into the open entity transaction so partial work commits atomically with the failure marker. `analyze::run` is annotated `#[allow(clippy::too_many_lines)]` — the seams are documented with banner comments, the author clearly sees them. The risk is the unique-to-this-branch invariant: entity inserts and the `failed` marker share a single SQLite transaction. The other two branches (`Completed`, `HardFailed`) are tested; the soft-fail middle is not. **Recommendation:** add `tests/analyze.rs` coverage for `Completed-with-crash → CommitRun(Failed) with partial entity commit` before any extraction refactor. + +**H-2. Edge ontology is duplicated across three sites with no compile-time enforcement.** +Catalog: `clarion-storage` §Concerns. `STRUCTURAL_EDGE_KINDS` + `ANCHORED_EDGE_KINDS` are hard-coded at `writer.rs:394–401`; the Python plugin's manifest declares `edge_kinds = ["contains", "calls", "references"]` independently at `plugin.toml:38`; ADRs 026/028 are the design source. Adding a kind requires edits in all three places; no test fails when only one moves. The host handshake catches manifest/manifest skew but not manifest/writer skew. **Recommendation:** lift `EdgeKindRegistry` to `clarion-core` so both the writer and the manifest validator consume one definition; alternatively, a unit test that builds the manifest's `edge_kinds` set and asserts it is a subset of the writer's hard-coded constants. + +**H-3. The ADR-024 single-migration retirement trigger is on manual discipline.** +Catalog: `clarion-storage` §Concerns. The migration file (`0001_initial_schema.sql:10–16`) documents the trigger ("when an external operator builds `.clarion/clarion.db` from a published Clarion build") but no automated check fires. Three documented edits already (initial; 2026-05-03 ADR-024 vocabulary rename; 2026-05-18 ADR-031 CHECKs). A fourth edit that adds a column when an external Clarion build is in the wild silently breaks downstream operators. **Recommendation:** file a Filigree tracker entry for the trigger condition; ideally surface via a CI guard that fails when the migration file is modified after a published-build marker (a `published_build.txt` or git tag). + +### 5.2 Medium — worth a follow-up issue + +**M-1. One MCP raw SQL site bypasses `clarion-storage`.** +Catalog: `clarion-mcp` §Concerns. `clarion-mcp/src/lib.rs:2470` (inside `reference_neighbors` declared at line 2455) is the only `conn.prepare(` site in the crate; everything else routes through typed query helpers in `clarion-storage::query`. A schema change to `edges` (column rename, ADR-026 kind addition) would not surface as a `clarion-storage` test failure. **Recommendation:** push `reference_neighbors` into `clarion-storage::query` with a typed result row; this keeps the storage layer the single point where edge-table SQL evolves. + +**M-2. `BudgetLedger.blocked` is sticky for the lifetime of `ServerState`.** +Catalog: `clarion-mcp` §Concerns (`lib.rs:1180–1316`). Once any reservation overshoots, `blocked` flips true and every subsequent LLM tool returns `token-ceiling-exceeded` until process restart. No documented reset path; no surface to lift the ceiling. Matches a session-token semantic but is undocumented in the public API. **Recommendation:** either document the session semantic in the `clarion.yaml` operator docs OR expose an MCP admin tool `reset_budget` that requires a token-ceiling-exceeded precondition. + +**M-3. Python plugin's `ONTOLOGY_VERSION` is duplicated.** +Catalog: Python plugin §Concerns. `server.py:36` declares `ONTOLOGY_VERSION = "0.5.0"`; `plugin.toml:46` declares the same. No shared import. The handshake validates the manifest value, leaving the constant as silent skew. Same shape of duplication as H-2 but lower blast radius (single language plugin, single ADR). **Recommendation:** import from `tomllib` at startup; assert equality on first use. + +**M-4. Dead stateless `handle_tool_call` stub in MCP public API.** +Catalog: `clarion-mcp` §Concerns. `lib.rs:1701–1736` emits `tool-unimplemented` envelopes for every tool name. Reachable from the stateless `handle_json_rpc` (line 154) and `handle_frame` (line 1621) paths, which are exported. CLI uses `handle_frame_with_state` (the stateful path) so this is not a runtime defect inside Clarion, but it is a footgun in the public API. **Recommendation:** either remove the stateless tool-call surface from public exports, or forward to the stateful handlers behind a `OnceCell`-style state initialiser. + +**M-5. `source_excerpt` reads live disk, not the hashed snapshot.** +Catalog: `clarion-mcp` §Concerns. `lib.rs:2151` uses `std::fs::read_to_string` on the on-disk file path to build LLM prompt input. The cache key still uses the stored `content_hash`, so a stale read produces a cache miss with a fresh-but-misaligned prompt. `stale_semantic` covers structural drift but not source-text drift. **Recommendation:** either persist a hash-keyed snapshot of source excerpts at ingest time, or refuse the summary call when the file's current hash != the stored hash (returning a typed `content-drift` error that callers can act on). + +### 5.3 Lower — observed but bounded + +**L-1.** `--force` flag declared but unimplemented in `clarion install` (`cli.rs:17–18`; rejected at `install.rs:87–92`). Either implement or drop. +**L-2.** `clarion-cli` walks the source tree but does not honour `.gitignore` (P4 in-code at `analyze.rs:1078`); `SKIP_DIRS` is a coarse stopgap. At `elspeth` scale this likely means walking generated/vendored paths. +**L-3.** Hand-rolled date math (`civil_from_unix_secs` in `analyze.rs:1197–1220`; `days_from_civil` in `clarion-mcp/src/lib.rs:2306–2314`). Justified for Sprint 1 by avoiding `chrono`; with `dotenvy`, `blake3`, `uuid`, `tracing-subscriber` already in tree, the rationale is thinner. +**L-4.** AST is re-parsed once by `extractor.py` and once by `pyright_session._build_function_index` per `analyze_file`. At elspeth scale (~425k LOC Python) this is two AST walks per file. Not yet measured; B.8 is exactly where this would surface. +**L-5.** `clarion-cli` serve and analyze can run concurrently against the same `.clarion/clarion.db` (two writer-actor processes); correctness depends entirely on `clarion-storage` WAL + `busy_timeout=5000`. The CLI does not test this combination; the discipline is in `clarion-storage` and trusted from above. +**L-6.** `clarion-core/src/plugin/host.rs` has 14 `HostFinding` constructors at lines 450–637 inflating the file size; moving them to a sibling `host_findings.rs` would shave ~200 LOC without altering semantics. +**L-7.** Filigree `actor` header silently omitted when blank rather than rejected at config-load (`filigree.rs:94–96`). +**L-8.** No `Drop` cleanup for in-flight `broadcast::Sender` map entries on leader cancellation in MCP coalesced dispatch; low-probability leak, time-bounded by the 60-second wait. + +### 5.4 Risks the doctrine consciously accepts (do not "fix") + +**A-1.** Wardline soft-import asterisk (`wardline_probe.py:38`). Documented in `docs/suite/loom.md` §5 with a retirement condition. Sprint-1 lock-in. +**A-2.** Wardline → Filigree pipeline coupling routed through Clarion. Same §5 register. +**A-3.** `clarion-core/src/plugin/host.rs` size (3 126 LOC, prod 1 450). Coherent; banded; tests dominate; not a refactor priority. +**A-4.** `clarion-mcp/src/lib.rs` size (2 623 LOC). Coherent; banded (protocol surface → `ServerState` → per-tool handlers → LLM pipelines → transport loop → helpers). Worth subdivision on size grounds, not correctness grounds. The catalog calls out the five plausible standalone modules. + +--- + +## 6. Sprint-2 deltas and working-tree state + +(Source: `01-discovery-findings.md` §7; cross-validated by `git log` and `git status` at analysis time.) + +**Whole-of-Sprint-2.** Six merged feature work-packages plus the OpenRouter provider swap since `v0.1-sprint-1`: +- **B.2** — class + module entities (merge `e53191d`) +- **B.3** — contains edges (merge `f9bd31e`, ontology `0.3.0`) +- **B.4*** — calls edges + confidence tiers (merge `837d965`, ontology `0.4.0`) +- **B.5*** — references edges via pyright (merge `e988a83`, ontology `0.5.0`) +- **B.6** — seven-tool MCP surface (merge `ed64a16`) +- **B.8** — scale test on the `elspeth` corpus (sign-off `ffdfd79`, GREEN after one repair rerun) +- **OpenRouter swap** — replace Anthropic with OpenRouter (merge `35be4db`, infrastructure change, not a feature work-package) + +**Sprint hygiene** commits worth keeping in cache: `9ffc5c8` replaced `serde_yaml` with `serde_norway` (the safe YAML parser); `dc9bf41` made `.env` loading happen before tracing init; `a80c31a` added `.env` to `.gitignore`; `c7ec1dd` introduced ADR-031 CHECK clauses; `0cb61b4` fixed the manifest rule-ID grammar quantifier. + +**Current branch (`sprint-2/b8-scale-test`) vs. `main`** (at analysis-emit time, commit `363bb0a`). 17 commits ahead, 59 files changed, 25 650 insertions, 85 deletions. The bulk of insertions are committed test artifacts (B.8 scale-test result JSON snapshots, including new raw artifacts from `caa6459`); substantive source changes are modest: +- `crates/clarion-core/src/llm_provider.rs` +193 lines (OpenRouter strict-JSON path) +- `crates/clarion-mcp/src/lib.rs` +260 lines through `363bb0a` (B.8 follow-up — reservation-poison fix `87036b1` + inferred-target pre-filter `363bb0a`) +- `crates/clarion-storage/migrations/0001_initial_schema.sql` +33 lines (ADR-031 CHECK clauses) +- `crates/clarion-storage/tests/schema_apply.rs` +148 lines (new test verifying CHECK enforcement) +- `docs/clarion/adr/ADR-031-schema-validation-policy.md` +426 lines (new ADR) +- `plugins/python/src/clarion_plugin_python/extractor.py` +98 lines (B.8 `@overload`-stub skip + safety-net dedup) +- `plugins/python/tests/test_extractor.py` +184 lines + +**Working tree (not yet committed).** `git status` at analysis time shows seven modified files + one new ADR (`ADR-031`) + a B.8 result-snapshot directory (`tests/perf/b8_scale_test/results/2026-05-18T0017Z/`). The GREEN-rerun results are partially committed and partially still in the working tree — this is in-flight work, not stale. + +--- + +## 7. Recommended follow-ups (prioritised) + +Each item maps to a §5 entry. Recommend filing in Filigree under `release:v0.1`, `sprint:3`. + +| # | Priority | Item | Rationale | Effort | +|---|---|---|---|---| +| 1 | High | Add `SoftFailed`-branch integration test to `tests/analyze.rs` | H-1 — unique transaction invariant currently uncovered | S | +| 2 | High | Unify edge-kind registry across writer / manifest / ADR | H-2 — silent skew risk on Sprint-3 ontology additions | M | +| 3 | High | Filigree tracker for ADR-024 migration retirement condition | H-3 — manual discipline at risk when external operators arrive | XS | +| 4 | Medium | Push `reference_neighbors` SQL into `clarion-storage::query` | M-1 — schema-coupling outside the storage layer | S | +| 5 | Medium | Decide on session-budget reset semantic + document | M-2 — operator surprise after one ceiling breach | S | +| 6 | Medium | Single-source `ONTOLOGY_VERSION` in Python plugin (read `plugin.toml` at startup) | M-3 — same shape as H-2, lower blast radius | XS | +| 7 | Medium | Remove or fold the stateless `handle_tool_call` MCP stub | M-4 — public-API footgun | XS | +| 8 | Medium | Decide `source_excerpt` policy: snapshot at ingest, or refuse on drift | M-5 — correctness drift in LLM prompts under file edits | M | +| 9 | Low | Implement or remove `clarion install --force` | L-1 | XS | +| 10 | Low | `.gitignore`-aware source walk | L-2 — relevant at elspeth-scale | M | +| 11 | Low | Decide on `chrono` adoption vs. keep hand-rolled date math | L-3 | XS | +| 12 | Low | Measure AST re-parse cost at elspeth scale (B.8 telemetry) | L-4 | S | +| 13 | Low | Document or test concurrent `serve` + `analyze` against one DB | L-5 | M | +| 14 | Low | Move `HostFinding` constructors to a sibling module | L-6 — cosmetic | XS | +| 15 | Low | Reject blank Filigree `actor` at config-load | L-7 | XS | +| 16 | Low | `Drop` cleanup for `inferred_inflight` map entries | L-8 — bounded leak | S | + +(Carryover items from Sprint 1, listed in `CLAUDE.md` and not duplicated here: `clarion-48c5d06578` supervisor drain/discard; `clarion-928349b60f` jail TOCTOU; `clarion-35688034f0` read_frame deadline; `clarion-c0977ac293` RLIMIT_AS end-to-end observation; `clarion-adeff0916d` fixture-binary self-build. These should be triaged into Sprint-3 alongside §5's new finds.) + +--- + +## 8. Confidence and limitations + +### Confidence summary + +| Aspect | Confidence | Basis | +|---|---|---| +| Crate boundaries + dependency graph | **High** | `Cargo.toml` workspace + `use clarion_*::` grep per crate | +| File-level structure of every subsystem | **High** | Per-subsystem agent read each crate's `src/*.rs` modules in full or near-full; LOC totals verified by `wc -l` | +| ADR alignment claims | **High where ADR-cited; Medium where inferred** | ADRs 002/003/007/011/021/022/023/024/026/027/028/029/030/031 read or quoted; ADR text not re-opened in every subsystem pass | +| LLM dispatch path correctness | **High** | Cache-key construction sites cited in both `clarion-mcp::lib.rs` and `clarion-storage::cache`; ADR-007 5-tuple verified literal-for-literal | +| Sprint-2 deltas | **High** | `git log v0.1-sprint-1..HEAD` + `git diff --stat main..HEAD` + `git status` | +| Quality / aesthetic judgments | **Out of scope** | This pass produces description, not assessment; see `axiom-system-architect:assess-architecture` for an opinionated quality review | + +### Limitations and information gaps + +- **Test coverage is not depth-read.** Test files were enumerated and sampled (signatures, top-level test names); no test was read end-to-end. Claims like "no `SoftFailed` integration coverage" rely on file-signature inspection, not function-by-function reading. +- **External siblings (Filigree, Wardline) are not vendored.** Cross-product claims rely on manifest pins (`min_version = "1.0.0"`, `max_version = "2.0.0"`) plus the doctrine memos under `docs/suite/`. The actual sibling repo state was not inspected. +- **The `scripts/` directory** was inventoried by `ls` only (one bash + small helpers per discovery); not deep-read this pass. +- **B.8 scale-test result data** (~22 000 lines of JSON snapshots in `tests/perf/b8_scale_test/results/`) was not inspected. Only the harness (`driver.py`) was sampled for shape, and the sign-off (`docs/implementation/sprint-2/b8-results.md`) was read. +- **One catalog contradiction was corrected during validation** (the `clarion-core` entry incorrectly stated `clarion-plugin-fixture` does not depend on `clarion-core`; the actual dep is on `clarion-core` types only and was corrected in-place). One minor LOC drift was footnoted (`clarion-mcp/src/lib.rs` 2 620 → 2 623). No other factual discrepancies survived the validation pass. + +### Audit trail + +``` +docs/arch-analysis-2026-05-18-1244/ +├── 00-coordination.md coordination plan + execution log +├── 01-discovery-findings.md holistic scan (384 lines, single explorer) +├── 02-subsystem-catalog.md 6 entries (~650 lines, 5 parallel explorers) +├── 03-diagrams.md 5 Mermaid diagrams (this coordinator) +├── 04-final-report.md this report (this coordinator) +└── temp/ + ├── section-*.md 6 raw section files from subsystem agents + ├── validation-02-subsystem-catalog.md NEEDS_REVISION (warnings) → fixed + └── validation-03-diagrams.md APPROVED +``` + +Subagent identities used: `axiom-system-archaeologist:codebase-explorer` (6 instances, 5 in parallel + 1 for discovery); `axiom-system-archaeologist:analysis-validator` (2 instances — catalog + diagrams). diff --git a/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-cli.md b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-cli.md new file mode 100644 index 00000000..926787d7 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-cli.md @@ -0,0 +1,108 @@ +## clarion-cli + +**Location:** `crates/clarion-cli/` + +**Responsibility:** Glue binary for the `clarion` executable; `clap`-driven subcommand dispatch (`install`, `analyze`, `serve`) that wires `clarion-core` (plugin host, LLM provider), `clarion-storage` (writer-actor + reader-pool), and `clarion-mcp` (stdio server) into a single end-user tool, and converts the storage layer's `RunStatus` taxonomy into shell exit codes. + +**Key Components:** + +- `src/main.rs` (33 lines) — process entry. Loads `.env` via `dotenvy::dotenv()` from CWD or any ancestor *before* `init_tracing()` so a `.env`-supplied `RUST_LOG` is in effect by the time the `EnvFilter` is built (commit `dc9bf41`, `main.rs:16–17`). Parses `cli::Cli`, then dispatches: `Install` and `Serve` run synchronously, `Analyze` builds an ad-hoc multi-thread `tokio::runtime::Builder` and `block_on`s `analyze::run(path)` (`main.rs:21–26`). No top-level runtime — each subcommand owns its own concurrency story. + +- `src/cli.rs` (43 lines) — `clap` derive structs only. `Install { --force, --path=. }`, `Analyze { path=. }`, `Serve { --path=., --config=Option }`. `--force` is declared but documented in code as "not implemented in Sprint 1" (`cli.rs:17–18`). + +- `src/install.rs` (168 lines) — `.clarion/` bootstrap. Refuses if the dir already exists (`install.rs:104–110`); refuses if `--force` is passed because Sprint-1 never implemented overwrite (`install.rs:87–92`). On `mkdir` success delegates to `populate_after_mkdir`, which (a) opens `clarion.db`, applies `clarion_storage::pragma::apply_write_pragmas` then `clarion_storage::schema::apply_migrations` (`install.rs:162–167`), (b) writes a stub `config.json` (`schema_version: 1, last_run_id: null`, `install.rs:22–26`), (c) writes a `.gitignore` carrying ADR-005's tracked-vs-excluded rules (`install.rs:54–77`), (d) writes a substantive `clarion.yaml` stub at project-root with LLM and Filigree-integration scaffolding (`install.rs:28–52`). Crucially, `clarion.yaml` is left untouched if it already exists (`install.rs:150–158`). Includes a cleanup guard: any failure inside `populate_after_mkdir` triggers `fs::remove_dir_all(.clarion)` before bubbling the error so the next attempt isn't blocked by the existence check (`install.rs:117–127`; references issue `clarion-ed5017139f`). + +- `src/serve.rs` (136 lines) — MCP stdio server wiring, in this exact sequence (`serve.rs:14–91`): (1) assert `.clarion/clarion.db` exists or hint the operator to run `install` first (`serve.rs:15–21`); (2) canonicalise the project root; (3) read `clarion.yaml` via `McpConfig::from_path` or default to `McpConfig::default()` (`serve.rs:26–33`); (4) resolve provider selection via `select_provider_with_env` with a `std::env::var` closure (`serve.rs:34`); (5) build the `Arc` via local `build_llm_provider` — `Disabled`/`Recording` (loads JSON fixture from `config.llm.recording_fixture_path` relative to project_root, `serve.rs:122–136`) / `OpenRouter` (passes `api_key`, `allow_live_provider: true`, model id, endpoint, and the attribution Referer/Title); (6) build the optional `FiligreeHttpClient::from_config` (`serve.rs:36–39`); (7) lock `stdin`/`stdout` and wrap stdin in `BufReader`; (8) build a **single-thread current-thread** tokio runtime, `runtime.enter()` as a guard so spawned tasks attach; (9) open the `ReaderPool` (size 16, `serve.rs:50`); (10) construct `ServerState::new(project_root, readers)`; (11) if a provider exists, spawn an LLM-only `Writer` against the same db_path with `DEFAULT_BATCH_SIZE`/`DEFAULT_CHANNEL_CAPACITY` and attach it via `state.with_summary_llm(writer.sender(), config.llm.clone(), provider)` (`serve.rs:55–65`); (12) if the Filigree client built, attach via `state.with_filigree_client(Arc::new(client))` (`serve.rs:66–68`); (13) hand off to `clarion_mcp::serve_stdio_with_state_on_runtime` (`serve.rs:70–72`); (14) drop `state`, drop `llm_writer` to close its sender, `runtime.block_on(handle)` to join the writer (`serve.rs:73–84`); (15) propagate `serve_result?` then the writer's `result?` so a clean MCP loop still fails the process if the writer errored. + +- `src/analyze.rs` (1436 lines) — the orchestrator. Internal structure, in source order: + + - **Public entry `pub async fn run(project_path: PathBuf)` (`analyze.rs:40–542`)** — single ~500-line function flagged `#[allow(clippy::too_many_lines)]`. Phases (clearly demarcated by `── … ──` banner comments): + 1. Path validation + `.clarion/` existence check (`:41–56`). + 2. **Writer actor lifecycle — open**: `Writer::spawn(db_path, DEFAULT_BATCH_SIZE, DEFAULT_CHANNEL_CAPACITY)` returns a `(writer, handle)` pair; mints a `Uuid::new_v4()` run id and `BeginRun` via `writer.send_wait(...)` (`:60–75`). + 3. **Plugin discovery** via `clarion_core::discover()`; successes pushed into `plugins`, failures collected into `discovery_errors` (`:78–97`). + 4. **No-plugins branch** (`:99–171`): distinguishes "zero discovered + zero errors" (`SkippedNoPlugins` via `CommitRun`, exits 0 with a "skipped_no_plugins" stdout line) from "zero usable + non-empty errors" (`FailRun` with the concatenated error list, then `bail!` for non-zero exit). The fix for hiding manifest-parse bugs as `SkippedNoPlugins` is explicit in the comment at `:100–103`. + 5. **Extension union + source walk** — collect_source_files walks once over the union of every plugin's declared extensions (`:174–184`). + 6. **Per-plugin loop** (`'plugins:` label, `:211–412`): filter the global file list to this plugin's extensions; if empty, `continue`. Otherwise dispatch a `tokio::task::spawn_blocking(move || run_plugin_blocking(...))` and route its `JoinResult` through `handle_plugin_task_join_result` (which normalises a `JoinError` panic into a crash-reason string rather than `?`-propagating, `:259–271`, regression-tested as `clarion-cf17e4e779`). On `Err(reason)`: push into `crash_reasons`, tick `CrashLoopBreaker::record_crash`, and `break 'plugins` if `CrashLoopState::Tripped` (`:274–292`). On `Ok(BatchResult { entities, edges, unresolved_call_sites, stats, findings })`: fold per-batch stats into per-run accumulators; log every `HostFinding` individually (`:312–327`); flush entities then unresolved call-site replacements (`WriterCmd::ReplaceUnresolvedCallSitesForCaller`) then edges to the writer-actor in that exact order (`:341–391`). Any writer `send_wait` error stops the per-plugin loop and sets `run_outcome = HardFailed { reason }` (`:392–402`). + 7. **`RunOutcome` resolution** (`:421–522`) — `enum RunOutcome { Completed, SoftFailed { reason }, HardFailed { reason } }` at `:558–563`. Promotion rule: `Completed` + non-empty `crash_reasons` → `SoftFailed` so the entity batch still commits *and* the run row marks failed (`:421–429`). Snapshots `writer.dropped_edges_total` and `writer.ambiguous_edges_total` (atomic counters held on the `Writer` handle) and `pyright_latency.p95_ms()` into the stats JSON (`:435–441`). The three terminal branches dispatch: + - `Completed` → `WriterCmd::CommitRun { status: RunStatus::Completed, … }` + - `SoftFailed { reason }` → `WriterCmd::CommitRun { status: RunStatus::Failed, … }` plus `"failure_reason": reason` in the stats JSON; the writer folds `UPDATE runs SET status='failed'` into the open entity tx so the partial work commits atomically with the failure marker (`:478–509`, comment at `:551–553`). + - `HardFailed { reason }` → `WriterCmd::FailRun` — rolls back the open tx (`:510–521`). + 8. **Writer-actor lifecycle — close**: `drop(writer)` closes the command channel; `handle.await` joins the actor task (`:524–528`); on any `fail_reason`, `bail!` for non-zero exit — the run row is already correctly marked, this is purely about surfacing failure to the shell (`:530–534`). + + - **`run_plugin_blocking` (`:646–759`)** — synchronous worker that `spawn_blocking` runs. Spawns the plugin via `PluginHost::spawn`; loops `host.analyze_file(file)` for each file in the per-plugin extension-filtered list; accumulates entities, edges, per-file `AnalyzeFileStats`, and per-file unresolved call sites; on the happy path tries `host.shutdown()` and falls back to `child.kill()` if shutdown writes to a closed pipe (`:731–742`); always `reap_and_classify_exit(&mut child, ...)` afterwards because `std::process::Child::Drop` does not `wait()` on Unix and would leak zombies (`:746–747`, comment at `:641–645`). + + - **`reap_and_classify_exit` (`:769–815`)** — on `signal() == SIGKILL (9)` or `SIGSEGV (11)` appends `HostFinding::oom_killed(plugin_id, signal)` per ADR-021 §2d; other signals or non-zero exits get a `warn` log but no finding. + + - **`classify_host_error` (`:818–843`)** — the explicit `HostError` → `String` mapping for fail-run reasons. Match arms: `EntityCapExceeded(_)` ("exceeded entity-count cap"), `PathEscapeBreakerTripped` ("tripped path-escape breaker"), `Spawn(msg)`, `Handshake(me)`, `Transport(te)`, `Protocol(pe)` (formats `code` + `message`), wildcard `other`. + + - **Entity/edge mapping** (`:846–946`) — `map_entity_to_record` derives `short_name` by rsplit('.'), serialises `entity.raw.extra` into `properties_json`, computes `content_hash` via local `content_hash_for_entity` (BLAKE3 over full file bytes for `module` kind, over normalised joined source lines `[start_line-1..end_line]` otherwise — `:907–927`). `map_edge_to_record` is a near-direct field-copy. Worth noting: `source_byte_start`/`source_byte_end` are hard-coded to `None` on entities — only the line range is captured. Edges keep byte ranges. + + - **Unresolved call-site bookkeeping (B.4*)** (`:948–1055`) — `map_unresolved_call_sites_for_file` groups sites by caller; checks "authoritative" mode (where `stats.unresolved_call_sites_total == stats.unresolved_call_sites.len()`) and pre-creates empty `PendingUnresolvedCallSites` for every function entity in the batch so the writer's `ReplaceUnresolvedCallSitesForCaller` can clear stale rows for callers that no longer have any unresolved sites. `validate_unresolved_call_site` enforces non-negative ordinal, non-empty/`<=512`-byte callee_expr, monotone byte range. `unresolved_call_site_key` is a BLAKE3 of `caller_entity_id || start_be || end_be || callee_expr`. + + - **Source-tree walk** (`:1063–1170`) — `walk_dir` is hand-rolled `std::fs::read_dir` recursion (no `walkdir` dep), with `SKIP_DIRS = [".clarion",".git",".hg",".svn",".jj",".venv","__pycache__","node_modules"]`, symlink skipping, and per-entry I/O error counting (skipped entries are tallied and surfaced as one summary `warn` line at end of walk to avoid silent partial analysis). **Does not honour `.gitignore`** — flagged P4 at `:1078`. + + - **Time helpers** (`:1180–1220`) — hand-rolled `iso8601_now()` using Howard Hinnant's `civil_from_days`, to avoid bringing in `chrono` for one format string. + +- `src/stats.rs` (37 lines) — `pub(crate) struct P95Accumulator { samples_ms: Vec }` with `record_many` and a nearest-rank `p95_ms()` (`stats.rs:21`). Sole client is the pyright-query-latency rollup in `analyze.rs`. + +**Integration tests** (`crates/clarion-cli/tests/`, 1217 LOC total): +- `install.rs` (247 lines) — black-box `assert_cmd` cases covering `.clarion/` contents, `.gitignore` rule presence, refusal-on-existing, `--force` refusal. +- `analyze.rs` (389 lines) — black-box analyze coverage. +- `serve.rs` (213 lines) — runs `clarion serve` as a child process, frames JSON-RPC bodies via `clarion_core::plugin::{Frame, read_frame, write_frame}` (re-exported through the `plugin` facade for test consumers), exercises the MCP `initialize` round-trip and `summary` tool dispatch (it imports `LEAF_SUMMARY_PROMPT_TEMPLATE_ID`). +- `wp1_e2e.rs` (74 lines) — WP1 walking-skeleton; mostly install/analyze sanity. +- `wp2_e2e.rs` (494 lines) — WP2 walking-skeleton consuming the on-disk `clarion-plugin-fixture` binary (declared as a `[dev-dependencies]` workspace member in `Cargo.toml:33`). + +**Dependencies:** + +- Inbound: + - End-users / shell / CI (the binary). + - `tests/e2e/sprint_1_walking_skeleton.sh` and `tests/e2e/sprint_2_mcp_surface.sh` invoke it as a subprocess. + - `tests/perf/b8_scale_test/driver.py` (B.8 scale-test harness) invokes it as a subprocess. + - No Rust-level inbound deps — this is a `[[bin]]`-only crate and exposes no library API (`Cargo.toml:12–14`). + +- Outbound: + - `clarion-core` — `PluginHost`, `discover`, `Manifest`, `DiscoveredPlugin`, `AcceptedEntity`/`AcceptedEdge`, `AnalyzeFileOutcome`, `AnalyzeFileStats`, `UnresolvedCallSite`, `CrashLoopBreaker`/`CrashLoopState`, `HostError`, `HostFinding`, `FINDING_DISABLED_CRASH_LOOP`, `LlmProvider`, `OpenRouterProvider`/`OpenRouterProviderConfig`, `Recording`/`RecordingProvider` (used in `analyze.rs:19–23`, `serve.rs:7–9`). + - `clarion-storage` — `Writer`, `ReaderPool`, `WriterCmd`, `EntityRecord`, `EdgeRecord`, `RunStatus`, `UnresolvedCallSiteRecord`, `DEFAULT_BATCH_SIZE`/`DEFAULT_CHANNEL_CAPACITY`, `pragma`, `schema` (used in `analyze.rs:24–27`, `install.rs:20`, `serve.rs:12`). + - `clarion-mcp` — `ServerState`, `config::{McpConfig, ProviderSelection, select_provider_with_env}`, `filigree::FiligreeHttpClient`, `serve_stdio_with_state_on_runtime` (used in `serve.rs:10–11, 52, 71`). + - Third-party: `clap` (derive CLI), `tokio` (runtime + `spawn_blocking` + `block_on`), `anyhow` (error type), `tracing` + `tracing-subscriber` (with `EnvFilter`), `dotenvy` (env loading), `uuid` (run IDs), `blake3` (content hashes + unresolved-site keys), `rusqlite` (install-time direct connection only — analyze and serve go through `Writer`/`ReaderPool`), `serde_json`. + +**Patterns Observed:** + +- **Pattern A buffering** (documented at `analyze.rs:7`): plugin work runs synchronously inside `spawn_blocking`, returns a `BatchResult` to the async caller, and only then does the caller emit `WriterCmd::Insert{Entity,Edge}` over the writer-actor channel. The blocking task never touches the writer directly. +- **Tri-state run outcome** (`Completed` / `SoftFailed` / `HardFailed`): explicitly distinguishes "plugin crashed but other plugins' entities should still persist" (SoftFailed → `CommitRun(Failed)`) from "writer-actor itself is broken" (HardFailed → `FailRun`). Comment at `:543–556` is load-bearing — the chosen WriterCmd differs by branch. +- **Atomic claim+transition style errors**: `JoinError` is *not* `?`-propagated; it's intercepted by `handle_plugin_task_join_result` and reshaped into a crash reason so the run-row resolution machinery still fires. The bypass regression is named in code (`clarion-cf17e4e779`) at `:1230–1236`. +- **Best-effort cleanup with auditable fallback**: `install.rs` removes a partial `.clarion/` on bootstrap failure and logs (not bails) if cleanup itself fails; `analyze.rs::run_plugin_blocking` always reaps the child even on the kill path. +- **Single-thread current-thread runtime for stdio loops, multi-thread for analyze**: `serve.rs:45–48` deliberately uses `Builder::new_current_thread()` (the stdin loop is the only thing actually running); `main.rs:22–25` uses `new_multi_thread` for analyze because `spawn_blocking` needs a worker thread. +- **Direct schema apply in install, writer-actor everywhere else**: `install.rs` opens its own `rusqlite::Connection` to run pragmas + migrations (the writer-actor doesn't exist yet at install time); after that, every write goes through `WriterCmd::*`. +- **Stats JSON is structured but stringified**: `CommitRun.stats_json` is built via `serde_json::json!` and then `.to_string()` (`analyze.rs:452–465`), matching `clarion-storage`'s `String` field signature. + +**Concerns:** + +- **`analyze::run` is a single ~500-line `async fn` with `#[allow(clippy::too_many_lines)]` at `:39`.** It mixes plugin discovery, file walking, per-plugin orchestration, writer-actor lifecycle, crash-loop policy, and three-way outcome resolution. The phase banners (`── Writer actor ──`, `── Discover plugins ──`, etc.) prove the author recognised the seams; extracting at least the per-plugin loop and the outcome-resolution match into named helpers would reduce the cognitive cost and make adding a fourth `RunOutcome` variant safer. +- **`source_byte_start` / `source_byte_end` are hard-coded `None` on entity records** (`analyze.rs:873–874`). The schema columns exist (`EntityRecord` carries them) and edges do populate them. Either the plugin should emit byte offsets and the CLI should plumb them, or the entity columns are documented dead weight. +- **Hand-rolled date math** (`civil_from_unix_secs`, `:1197–1220`) was justified for Sprint 1 by avoiding `chrono`. With `dotenvy`, `blake3`, `uuid`, and `tracing-subscriber` already in tree, the "we don't have a date dep" rationale is thinner now; the comment at `:1175–1179` itself anticipates promoting `chrono` "at that point." Worth a follow-up issue. +- **The source walk does not honour `.gitignore`** (P4 noted in-code at `:1078`). On the `elspeth` corpus this likely means walking generated and vendored code paths the operator considers out-of-scope. `SKIP_DIRS` is a coarse stopgap. +- **`install.rs::initialise_db` opens a connection, applies pragmas + migrations, and lets it drop without an explicit close.** SQLite handles this safely (the dtor closes the handle and flushes WAL), but the symmetry with the writer-actor's explicit `Drop` and the explicit ordering elsewhere makes this stand out. Not a defect; a stylistic gap. +- **Serve's LLM writer is independent from the analyze writer.** When `clarion serve` is up *and* `clarion analyze` is run in another process, two `Writer` actors hold connections to the same `clarion.db`. The pragma layer (WAL + `busy_timeout`) is what keeps that safe — this is a `clarion-storage` invariant the CLI relies on but doesn't enforce or test in the cli-tests. Worth verifying in the storage subsystem brief. +- **`--force` accepted but unimplemented.** `install.rs:87–92` rejects the flag with a `bail!`. Sprint-2+ has not implemented the overwrite path despite the `cli.rs:17` doc-comment hinting at one. If the operator workflow has stabilised, either implement it or remove the flag. +- **No integration test exercises the `SoftFailed` path end-to-end.** `analyze.rs` tests cover `Completed` and `SkippedNoPlugins`; the soft-fail branch (where one plugin crashes but another succeeds) is the most subtle path — it's the one where an entity batch and a `status='failed'` UPDATE share a single SQLite transaction — and no `tests/analyze.rs` case (per a `grep` of the test file's signatures, not deep-read this pass) targets it. The crash-loop unit tests inside `analyze.rs:tests` cover `handle_plugin_task_join_result` but not the writer side of the soft-fail folding. + +**Confidence:** High — read `main.rs`, `cli.rs`, `install.rs`, `serve.rs`, `stats.rs`, and `Cargo.toml` in full; read `analyze.rs:1–542` (the full async `run`), `:559–815` (RunOutcome, JoinError helper, BatchResult/BatchStats/PendingUnresolvedCallSites structs, run_plugin_blocking, reap_and_classify_exit), `:818–843` (classify_host_error), `:846–946` (entity/edge mapping + content hashing), `:948–1055` (unresolved-call-site mapping), `:1057–1170` (source walk), and `:1180–1220` (time helpers). Cross-validated outbound deps by reading the import block at `analyze.rs:19–27`, `serve.rs:7–12`, `install.rs:20`; confirmed against `Cargo.toml:17–29`. Sample of test headers read for `tests/install.rs` and `tests/serve.rs`. Phase-level walkthrough of `analyze::run` annotated with line ranges throughout. The five open questions in the brief are answered in the text above with file:line citations. + +**Risk Assessment:** + +- **God-function risk on `analyze::run`** (high likelihood, medium impact). Length is already a documented smell. Mitigation: extract the per-plugin loop and outcome resolution; add `SoftFailed` integration coverage before extraction so the refactor has a regression net. +- **Stale CLI surface risk** (low likelihood, low impact). `--force` advertised but unimplemented; could mislead a CI author. Mitigation: implement or remove. +- **Multi-process writer correctness** (low likelihood, high impact). Two `Writer` actors against one DB rely on `clarion-storage` pragma discipline (WAL + `busy_timeout`). The CLI is the only place this combination is wired in production. Mitigation: a serve+analyze concurrent integration test would prove the invariant from the CLI side; right now the discipline is owned by `clarion-storage` and trusted by the CLI. + +**Information Gaps:** + +- `tests/analyze.rs` (389 lines) was not deep-read this pass; the claim that no test exercises the `SoftFailed` path is based on the test file's signature surface and the comments in `analyze.rs`, not on a function-by-function read. A follow-up could promote that claim from "likely" to "verified" or refute it. +- `select_provider_with_env`'s exact precedence (env-var override of YAML vs YAML wins) is `clarion-mcp::config`'s concern, not visible from CLI source. The CLI passes a `|name| std::env::var(name).ok()` closure (`serve.rs:34`) and trusts the resolver. +- Whether the LLM `Writer` spawned in `serve.rs` and the `analyze` `Writer` would conflict on the same `clarion.db` was not verified end-to-end — only that pragma discipline in `clarion-storage` is intended to absorb it. + +**Caveats:** + +- Line counts include `#[cfg(test)]` blocks where present in `src/`. `analyze.rs:1224+` contains an in-source `mod tests` whose contents were not deep-read beyond the `handle_plugin_task_join_result` regression comment. +- The `clarion.yaml` stub written by `install` (`install.rs:28–52`) commits the CLI to a specific config shape (model id `anthropic/claude-sonnet-4.6`, default Filigree port `8766`, default OpenRouter endpoint). Those defaults belong to the operator config story, not the CLI's responsibility surface — flagged here only as a fact, not a critique. +- No code-quality assessment is made — that is an `axiom-system-architect:assess-architecture` concern. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-core.md b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-core.md new file mode 100644 index 00000000..482cc433 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-core.md @@ -0,0 +1,132 @@ +## clarion-core + +**Location:** `crates/clarion-core/` + +**Responsibility:** Owns the canonical entity-ID grammar, plugin-host subprocess supervisor + JSON-RPC peer, LLM-provider trait + OpenRouter implementation, plugin-manifest parser, and the jail / RSS / entity / breaker ceilings that every other crate depends on for safety. + +**Public interface:** + +`lib.rs` is 47 lines (see `crates/clarion-core/src/lib.rs:1-47`) and is explicit that it is a curated facade per ticket `clarion-29acbcd042`. Re-exports at the crate root, grouped by submodule: + +- **From `entity_id`**: `EntityId`, `EntityIdError`, free function `entity_id(plugin, kind, qualname)` — the cross-language assembler. +- **From `llm_provider`**: trait `LlmProvider`; `OpenRouterProvider` + `OpenRouterProviderConfig`; `RecordingProvider` + `Recording` (test fixture replay); error type `LlmProviderError`; request/response DTOs `LlmRequest` / `LlmResponse` / `LlmPurpose`; `CachingModel`; prompt builders `build_leaf_summary_prompt`, `build_inferred_calls_prompt`, with stable IDs `LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1"` and `INFERRED_CALLS_PROMPT_VERSION = "inferred-calls-v1"`. +- **From `plugin`**: `PluginHost`, `Manifest` + `parse_manifest`, `AcceptedEntity` / `AcceptedEdge` / `AnalyzeFileOutcome` / `AnalyzeFileStats`, `EdgeConfidence`, `UnresolvedCallSite`, `HostError` + `HostFinding`, `JailError`, `CapExceeded`, `DiscoveredPlugin` + `DiscoveryError` + `discover()`, `CrashLoopBreaker` + `CrashLoopState`, and the finding-ID constants (`FINDING_DISABLED_CRASH_LOOP` re-exported at root, with sibling `FINDING_*` constants reachable through `clarion_core::plugin::*`). + +Implementation types deliberately *not* re-exported at the root but still reachable via fully-qualified paths: transport (`Frame`, `read_frame`, `write_frame`, `TransportError`), protocol envelopes (`RequestEnvelope`, `ResponseEnvelope`, `AnalyzeFileParams`, etc.), prlimit helpers, raw entity/edge structs. `make_notification` / `make_request` are `pub(crate)` — `mod.rs:38-42` explains they panic on serde failure and external callers should build envelopes directly. + +**Internal structure:** + +Top-level modules (`crates/clarion-core/src/`): + +- `entity_id.rs` (610 LOC) — `EntityId` newtype + `entity_id()` constructor + `EntityIdError`. Includes the cross-language parity test against `fixtures/entity_id.json` (ADR-003, L2 lock-in). +- `llm_provider.rs` (948 LOC) — single-file LLM abstraction. See breakdown below. +- `plugin/` — supervisor + protocol + safety primitives. Submodule roles documented inline at `plugin/mod.rs:1-12`: + - `manifest.rs` (1508 LOC) — `Manifest`, `PluginMeta`, `Capabilities`, `CapabilitiesRuntime`, `PyrightRuntime`, `Ontology`, `parse_manifest()`, kind-grammar + rule-ID-prefix validators (ADR-021/ADR-022, L5). + - `protocol.rs` (846 LOC) — JSON-RPC 2.0 typed envelopes; `AnalyzeFileParams/Result`, `AnalyzeFileStats`, `UnresolvedCallSite`, `EdgeConfidence`, `InitializeParams/Result`, `Shutdown`, `Exit`, `ProtocolError`. + - `transport.rs` (568 LOC) — `Frame`, `read_frame`/`write_frame`, Content-Length framing with `MAX_HEADER_LINE_BYTES = 8 KiB`; surfaces oversize via `TransportError`. + - `jail.rs` (253 LOC) — `jail()` / `jail_to_string()` canonicalises and asserts containment under project root; `JailError::{EscapedRoot, NonUtf8Path, Io}`. + - `limits.rs` (552 LOC) — `ContentLengthCeiling`, `EntityCountCap`, `PathEscapeBreaker`, `BreakerState`, the finding-ID constants for cap violations, and the Unix `apply_prlimit_as` / `apply_prlimit_nofile_nproc` (no-op stubs on non-Unix). `DEFAULT_MAX_RSS_MIB = 2048` (ADR-021 §2b ceiling). + - `breaker.rs` (360 LOC) — `CrashLoopBreaker`, `CrashLoopState`, `FINDING_DISABLED_CRASH_LOOP` (ADR-002 §UQ-WP2-10). + - `discovery.rs` (637 LOC) — `DiscoveredPlugin`, `DiscoveryError`, `discover()` (Linux only — non-Unix returns empty), `discover_on_path()`, scans `$PATH` for `clarion-plugin-*` executables and pairs them with a sibling `share/clarion/plugins//plugin.toml` (cap 64 KiB). + - `host.rs` (3126 LOC) — see below. + - `mock.rs` (897 LOC, `#[cfg(test)] pub(crate)`) — in-process mock plugin; reachable only from unit tests in this crate. + +### Internal organisation of `plugin/host.rs` (3126 LOC) + +Despite the line count, the file is **not a god-file** — it is structurally one struct (`PluginHost`) with two layers of constructors, an analyse-file pipeline, and a long unit-test suite. Concretely: + +- **Lines 1–155: Module-level constants and finding-ID strings** (`FINDING_*` for entity/edge ontology violations, plus byte caps `MAX_ENTITY_FIELD_BYTES = 4 KiB`, `MAX_ENTITY_EXTRA_BYTES = 64 KiB`, `MAX_UNRESOLVED_CALLEE_EXPR_BYTES = 512`). +- **Lines 157–345: Pure validators / decoders** (`effective_max_nproc`, `oversize_edge_field`, `oversize_field`, `invalid_unresolved_call_site_reason`). +- **Lines 346–438: Public DTOs** — `RawEntity`, `RawEdge`, `RawSource`, `AcceptedEntity`, `AcceptedEdge`, `AnalyzeFileOutcome`, `HostError` (with 17 variants covering Spawn, Handshake, Protocol, EntityCapExceeded, PathEscapeBreakerTripped, OomKilled, Io, etc.). +- **Lines 450–637: `HostFinding` + ~14 named constructors** (`undeclared_kind`, `entity_id_mismatch`, `path_escape`, `disabled_path_escape`, `entity_cap_exceeded_finding`, `unsupported_capability`, `non_utf8_path`, `malformed_entity`, `malformed_edge`, `undeclared_edge_kind`, `edge_field_oversize`, `malformed_unresolved_call_site`, `entity_field_oversize`, `oom_killed`). One constructor per finding type — the "constructor wall" inflates line count but is mechanical. +- **Lines 639–710: `PluginHost` struct definition + `drain_stderr_into_ring`** — generic over reader/writer so subprocess and in-process mock share one impl; `stderr_tail` is a 64 KiB ring buffer. +- **Lines 712–882: Subprocess constructor `PluginHost::spawn`** specialised to `BufReader` / `BufWriter`. This is the heaviest single function — it (1) validates manifest `executable` is a bare basename matching the discovered binary path (anti-redirect defence at host:756–780), (2) applies `RLIMIT_AS` + `nofile` + `nproc` via `pre_exec`, (3) spawns a detached stderr-drain thread, (4) reaps the child on handshake failure (host:864–880 — `Child::Drop` does *not* reap, so failure paths must explicitly wait). +- **Lines 883–957: `PluginHost::connect` + `new_inner` + accessors** (`stderr_tail`, `ontology_version`). +- **Lines 959–1028: `handshake()`** — the four documented steps: send `initialize`, validate response id, run `manifest.validate_for_v0_1()`, send `initialized`. On manifest failure the host is best-effort-shut-down without sending `initialized`. +- **Lines 1031–1198: `analyze_file()`** — the per-file orchestration pipeline. Reads as a numbered validator pipeline: + - `0.` field-size cap → oversize finding, drop (host:1103); + - `1.` ontology declared-kind check (host:1109); + - `2.` entity-id identity check (host:1116); + - `3.` path-jail check + path-escape breaker tick → kill-path on `Tripped` (host:1135); + - `4.` entity-cap check → kill-path on exceed (host:1166). +- **Lines 1200–1299: `process_edges()`** — same drop-on-violation posture, no kill paths (edges don't participate in breakers). +- **Lines 1300–1450: `process_stats`, `shutdown`, `take_findings`, `next_id`, `do_shutdown`, `read_response_matching`** (drain-until-match for stale frames at host:1398; idempotent shutdown via `terminated` flag at host:657). +- **Lines 1452–end (≈1700 LOC of tests)**: 30+ `#[cfg(test)]` named scenarios `t2_…` through `t9_…` plus B.3/B.4*/B.5* regressions. Tests dominate the line count; *production code in `host.rs` is ~1450 LOC*. + +The file is **coherent**: one supervisor type with one validator pipeline. The internal pressure to refactor is mild — splitting findings into a sibling module would shave ~200 LOC, but the drop-on-violation pipeline reads top-to-bottom and benefits from staying co-located. + +### Internal organisation of `llm_provider.rs` (948 LOC) + +Single-file LLM abstraction, organised top-to-bottom (no submodule because there is no `llm_provider/` directory): + +- **Lines 10–11: Stable prompt-ID constants** (`LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1"`, `INFERRED_CALLS_PROMPT_VERSION = "inferred-calls-v1"`). These form two of the five components of the ADR-007 cache key; the other three (`entity_id`, `content_hash`, `model_tier`, `guidance_fingerprint`) are assembled in `clarion-storage::cache::SummaryCacheKey`. **The 5-tuple is *not* materialised inside this file** — the provider is dispatch-only; cache keying happens in `clarion-storage` and `clarion-mcp`. +- **Lines 13–37: Request / response / purpose DTOs** (`LlmRequest`, `LlmResponse`, `LlmPurpose::{Summary, InferredEdges}`). +- **Lines 38–82: Error taxonomy** — `LlmProviderError` with six variants; `retryable()` returns the inner retryable flag for `Http`/`Provider`/`InvalidResponse`, false for `MissingRecording`/`LiveProviderNotAllowed`/`MissingApiKey`. +- **Lines 84–90: The `LlmProvider` trait** — five required methods: `name`, `invoke`, `estimate_tokens`, `tier_to_model`, `caching_model`. Trait is `Send + Sync` so providers can be shared across MCP request handlers behind an `Arc`. +- **Lines 92–151: `RecordingProvider`** — test-mode provider that replays exact-shape `LlmRequest` matches from a fixed `Vec`. Tracks invocations in a `Mutex>` for assertion. Returns `MissingRecording` (non-retryable) on shape drift. +- **Lines 153–295: `OpenRouterProvider`** — the live provider. + - Config gate at `from_config` (lines 173–187): requires both `allow_live_provider == true` AND a non-empty `api_key`; either failure yields `LiveProviderNotAllowed` / `MissingApiKey` (both non-retryable). + - `invoke()` (lines 202–279): blocking `reqwest` POST to `{endpoint}/chat/completions`, 60s timeout, `Authorization: Bearer`, `HTTP-Referer`, `X-OpenRouter-Title` headers. Payload includes `"temperature": 0`, `"provider": {"require_parameters": true}`, and `response_format` from `response_format_for_purpose()`. + - **The strict-JSON path** (the open question from §8) lives at `response_format_for_purpose` (lines 297–370): two JSON-Schema objects, both with `"strict": true` and `"additionalProperties": false`. `Summary` enforces `{purpose, behavior, relationships, risks}`; `InferredEdges` enforces `edges: [{site_key, target_id, confidence, rationale}]`. This is the B.8 GREEN-rerun fix from commit `ab6b1dd` — without `"strict": true` OpenRouter providers silently produced free-form text. + - Error unwrap chain: the response body is first parsed as `OpenRouterErrorEnvelope` (line 250) — even on HTTP 200, choices can carry per-call provider errors at `OpenRouterChatResponse::output_text` (line 379), which surfaces `LlmProviderError::Provider`. +- **Lines 297–500: HTTP plumbing** — response struct definitions (`OpenRouterChatResponse`, `OpenRouterChoice`, `OpenRouterMessage`, `OpenRouterUsage`, `OpenRouterErrorEnvelope`, `OpenRouterErrorBody`), `provider_error_from_body`, `retryable_status` (true for 408 / 429 / ≥500), `retry_after_seconds` (header parse), `estimate_text_tokens` (chars/4 heuristic). +- **Lines 502–561: Prompt builders** — `LeafSummaryPromptInput` / `InferredCallsPromptInput` DTOs and the two `build_*_prompt` functions emitting `PromptTemplate { id, body }`. Body is a hand-written `format!` template; no Tera/Handlebars. +- **Lines 563–end: Unit tests**, including a TCP-listener-based in-process OpenRouter stub at `openrouter_provider_invokes_chat_completions_and_extracts_usage_tokens`. + +**Nothing is cached inside `llm_provider.rs`.** The provider is a stateless dispatcher; caching is `clarion-storage::cache` (per discovery §4, Subsystem B) and lookup is performed by callers in `clarion-mcp::lib.rs` and the analyze-file inferred-edges path. Caching is *lazy and lookup-driven*: callers compute `SummaryCacheKey` from the 5-tuple, hit the cache, and only call `LlmProvider::invoke` on miss — then write the response back keyed on the same tuple. + +**Key types & traits:** + +| Type | Where | Why callers touch it | +|---|---|---| +| `EntityId`, `entity_id()` | `entity_id.rs` | Every accepted entity is identified by this; cross-language parity proof. | +| `LlmProvider` (trait) | `llm_provider.rs:84` | MCP and analyze layers receive `Arc` for dispatch. | +| `OpenRouterProvider`, `RecordingProvider` | `llm_provider.rs:164`, `:99` | Provider construction in `clarion-cli::serve.rs`. | +| `PluginHost` | `host.rs:639` | The per-file supervisor; `spawn` for production, `connect` for in-process tests. | +| `AcceptedEntity`, `AcceptedEdge`, `AnalyzeFileOutcome` | `host.rs:346–398` | Hand-off shapes from host → analyse orchestrator → writer-actor. | +| `Manifest` + `parse_manifest` | `manifest.rs:115`, `:281` | `clarion-cli::analyze` reads `plugin.toml` through this; `PluginHost` consumes it. | +| `CrashLoopBreaker` | `breaker.rs:43` | `clarion-cli::analyze` ticks this per plugin-spawn failure. | +| `discover()` / `DiscoveredPlugin` | `discovery.rs:133`, `:47` | Plugin discovery on `$PATH`. | +| `HostError` / `HostFinding` | `host.rs:400`, `:450` | Error matching + finding emission for operator diagnostics + Filigree forwarding. | +| `LlmProviderError` | `llm_provider.rs:44` | Caller uses `.retryable()` to drive WP6 backoff. | + +**Dependencies (workspace + outbound):** + +- **Inbound** (per `grep clarion-core` against each Cargo.toml): + - `clarion-storage/Cargo.toml:13` + - `clarion-mcp/Cargo.toml:13` + - `clarion-cli/Cargo.toml:20` + + *Note*: `clarion-plugin-fixture` does **not** depend on `clarion-core` — the fixture binary speaks the wire protocol directly without sharing types. This is deliberate (the discovery flagged the fixture is consumed only via subprocess in `wp2_e2e`). + +- **Outbound** (`Cargo.toml`): + - `reqwest` (workspace: `rustls-tls-native-roots`, blocking + JSON) — only `llm_provider.rs`. + - `serde` + `serde_json` + `toml` — DTO + manifest parsing. + - `thiserror` — every error enum here. + - `tracing` — host stderr-drain failures + best-effort-shutdown diagnostics. + - `nix` (workspace, `resource` feature only) — `apply_prlimit_*` in `limits.rs`. The single `unsafe` allowance in the workspace lives here (`pre_exec` + `setrlimit`); workspace lint floor is `unsafe_code = "deny"` (downgraded from `forbid` per documented exception in workspace `Cargo.toml`). + - `tempfile` (dev-dep) — tests only. + +- **Notably absent**: no `tokio` dependency. The plugin host is fully synchronous (`BufRead + Write` generic bounds, blocking `reqwest`). Async is introduced one layer up in `clarion-storage::writer` (`tokio::task`) and `clarion-mcp::lib.rs`. + +**Patterns observed:** + +- **Generic reader/writer typestate-lite** — `PluginHost` is generic; `spawn` returns a host parameterised on `BufReader` / `BufWriter`, while `connect` accepts any `BufRead + Write` pair so the in-process `mock.rs` and the e2e tests share one validator pipeline. +- **Drop-on-violation pipeline with discrete kill-paths** — `analyze_file` is a numbered five-step validator; steps 0–2 only emit findings and drop the offending record; steps 3–4 escalate to plugin termination if a breaker trips. The kill-paths route through a single `do_shutdown` (host:1352) that handles the idempotent-shutdown flag. +- **Newtype-with-constructor for safety-critical IDs** — `EntityId(String)` is private-field; the only constructors live in `entity_id.rs` and validate the grammar before producing the newtype. `FromStr` rebuilds via the same constructor. +- **Trait-object provider dispatch** — `Arc` consumed by MCP and analyze; live vs recording vs disabled selected at config time (`clarion-cli::serve.rs`). +- **Finding-ID constants as first-class API** — every `FINDING_*` is a `pub const &str` exported at module root so callers (and tests) can `assert_eq!` on the stable ID rather than match on free-form messages. The ID grammar (`CLA-INFRA-*`) is asserted at manifest-parse time (`manifest.rs:414`). +- **Pure-function validators** — `oversize_field`, `oversize_edge_field`, `invalid_unresolved_call_site_reason`, `validate_kind_string`, `validate_rule_id_prefix_grammar` are all stateless and unit-tested in isolation. + +**Concerns / risks:** + +- **`host.rs` size** (3126 LOC including ~1700 LOC of tests). Production code is ~1450 LOC and is coherent, but the file is the codebase's largest. A future refactor could move the 14 `HostFinding` constructors and the `FINDING_*` constants to a sibling `host_findings.rs` for ~200 LOC saved without altering semantics. +- **`manifest.rs` size** (1508 LOC) — not deep-read in this pass; the public type surface is small (one `Manifest` + five field-structs + one error enum + parser + two grammar validators). Likely test-dominated like `host.rs`, but worth a separate confirm pass. +- **Subprocess constructor is Linux-coupled** — `spawn` at `host.rs:739` uses `pre_exec` + `RLIMIT_AS`/`RLIMIT_NOFILE`/`RLIMIT_NPROC`. `limits.rs:330–342` provides no-op stubs for non-Unix targets, but `discover()` at `discovery.rs:139` is also `#[cfg(unix)]` and returns empty on Windows. v0.1 is Linux-only by intent (per Sprint-1 sign-off), but the cross-platform doors are stubs, not implementations. +- **Reqwest blocking inside a `Send + Sync` trait method** — `LlmProvider::invoke` is sync. Callers from async contexts (`clarion-mcp`) must `spawn_blocking`. Not verified in this pass which side actually does the offloading; if callers run `invoke` on the runtime thread, MCP tool handlers can starve. This belongs as a follow-up question for the `clarion-mcp` catalog pass. +- **OpenRouter strict-JSON regression risk** — the `"strict": true` JSON-Schema gates were added in commit `ab6b1dd` for B.8 GREEN; the path lives entirely in `response_format_for_purpose` (`llm_provider.rs:297`) and is asserted by a test that pattern-matches the serialised request body. A schema change anywhere in the prompt-output contract must update both the prompt template (`build_*_prompt`) and the strict-JSON schema in lockstep — there is no cross-check between them. +- **`unsafe` allowance lives here** — `pre_exec` + `setrlimit` is the workspace's sole `unsafe` block (documented in workspace `Cargo.toml`). Any new unsafe in `clarion-core` should require an ADR amendment. +- **No `tokio` use, but exported types flow into async runtimes** — `AcceptedEntity` / `AcceptedEdge` cross the async boundary via `clarion-storage::WriterCmd`. The DTOs are `Clone + Send` (verified through usage patterns) but this is not enforced by trait bounds at the public boundary; a future field that is not `Send` would silently break downstream. +- **Test-only `mock.rs` (897 LOC) lives inside `src/` under `#[cfg(test)]`** rather than in `tests/`. Pro: integration tests in `tests/wp2_e2e.rs` cannot link against it — keeping mock scaffolding off the public surface is exactly the goal (`mock.rs` is `pub(crate)`). Con: 897 LOC of test scaffolding inflates `clarion-core` source counts; deferred items include `clarion-adeff0916d` (fixture-binary self-build) which may consolidate this. + +**Confidence:** High — read `lib.rs` and `plugin/mod.rs` in full; read `host.rs` structural skeleton + `PluginHost` definition + `spawn` constructor + full `analyze_file` body; read `llm_provider.rs` in full through line 561 (the production code; tests sampled); cross-verified inbound deps via `grep clarion-core` against each crate's `Cargo.toml`. Two claims are Medium-confidence and called out above: (a) `manifest.rs` internal proportions not directly verified beyond signature scan; (b) whether MCP wraps `LlmProvider::invoke` in `spawn_blocking` is out-of-scope for this pass and listed as a follow-up. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-mcp.md b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-mcp.md new file mode 100644 index 00000000..e3f78904 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-mcp.md @@ -0,0 +1,103 @@ +## clarion-mcp + +**Location:** `crates/clarion-mcp/` + +**Responsibility:** Speaks MCP protocol revision `2025-11-25` over stdio; serves seven storage-backed read tools (`entity_at`, `find_entity`, `callers_of`, `execution_paths_from`, `summary`, `issues_for`, `neighborhood`) to consult-mode LLM agents, with on-demand LLM dispatch for leaf-scope summaries and inferred call edges, and optional Filigree enrichment for issue attachment. + +**Key Components:** + +- `src/lib.rs` (2620 LOC) — single-file crate root. Internal organisation, top-to-bottom: + - **Protocol surface** (lines 36–166): `MCP_PROTOCOL_VERSION = "2025-11-25"` constant (line 36), `ToolDefinition` struct (40–45), `list_tools()` returning seven hardcoded `ToolDefinition`s with inline JSON-Schema (48–120), schema helpers `confidence_schema` / `id_schema` / `id_confidence_schema` (122–151), stateless `handle_json_rpc` router (154–166) wired to `initialize` / `tools/list` / `tools/call`. + - **`ServerState`** (168–1252): the central handler. Fields (168–178): `project_root: PathBuf`, `readers: ReaderPool`, `execution_edge_cap: usize` (default 500), `summary_llm: Option`, `clock: Arc String + Send + Sync>`, `budget: Arc>`, `inferred_inflight: Arc>>>` (in-flight dispatch coalescing), `filigree_client: Option>`. Builder methods (180–226): `new`, `with_edge_cap`, `with_summary_llm`, `with_clock`, `with_filigree_client`. + - **Per-tool dispatch** (228–294): instance `handle_json_rpc` + `handle_tool_call` route by name to seven `tool_*` async methods. + - **Per-tool handlers** (296–717): `tool_entity_at` (296–319), `tool_find_entity` (321–354), `tool_callers_of` (356–391), `tool_execution_paths_from` (393–434) + `inferred_execution_paths` (436–520), `tool_neighborhood` (522–581), `tool_issues_for` (583–671), `tool_summary` (673–717). + - **LLM inferred-edges pipeline** (719–995): `ensure_inferred_for_target` / `ensure_inferred_for_caller` (719–796) — entry points called by `callers_of`/`neighborhood`/`execution_paths_from` when `confidence == Inferred`; `read_inferred_inputs` (798–833) builds an `InferredEdgeCacheKey` from caller content-hash + model_id + prompt_version (ADR-007); `materialize_cached_inferred` (835–863) on cache hit; `coalesced_inferred_dispatch` (865–908) deduplicates concurrent dispatches via a `broadcast` channel with a 60-second timeout; `perform_inferred_dispatch` (910–995) builds the prompt via `clarion_core::build_inferred_calls_prompt`, reserves budget, invokes the provider on a `spawn_blocking` task, then sends `WriterCmd::InsertInferredEdges` to the writer-actor. + - **LLM summary pipeline** (997–1155): `read_summary_inputs` (997–1035) keys against `SummaryCacheKey { entity_id, content_hash, prompt_template_id = LEAF_SUMMARY_PROMPT_TEMPLATE_ID, model_tier, guidance_fingerprint = "guidance-empty" }` — five-tuple cache key matching ADR-007; `cached_summary_envelope` (1037–1060) bumps `last_accessed_at` via `WriterCmd::TouchSummaryCache`; `refresh_summary` (1062–1155) on miss invokes provider, then `WriterCmd::UpsertSummaryCache`. ADR-030 leaf-scope is encoded by the single `LEAF_SUMMARY_PROMPT_TEMPLATE_ID` template and the `summary` tool description (line 98). + - **Writer-actor helper + budget** (1157–1251): `send_writer` (1157–1171) — oneshot ack roundtrip pattern; `BudgetLedger` accounting with `reserve_budget` / `BudgetReservation::commit` / `Drop` rollback (1180–1316); `summary_model_id` / `inferred_edges_model_id` / `max_inferred_edges_per_caller` (1221–1251) honour `LlmProvider::tier_to_model("summary"|"inferred_edges")`. + - **Plain types** (1266–1607): `SummaryLlmState`, `BudgetLedger`, `SummaryRead` enum, `SummaryReady`, `IssuesForRead`, `IssuesForAccumulator` (drift-classifier matching `content_hash_at_attach` against current `entities.content_hash`, lines 1379–1411, with 100-issue cap), `InferenceLlmState`, `InferredRead`, `InferredDispatchStats` (aggregated stats_delta), `InferredDispatchFailure`, `InferredDispatchOutcome`, `InferredCallsResponse` / `InferredCallsResponseEdge`. + - **Transport loop** (1609–1686): `McpError` enum, `handle_frame` / `handle_frame_with_state`, `serve_stdio` / `serve_stdio_with_state` / `serve_stdio_with_state_on_runtime` — Content-Length frame loop using `clarion_core::plugin::{read_frame, write_frame, ContentLengthCeiling::DEFAULT, Frame, TransportError}`; treats `UnexpectedEof` as clean shutdown. + - **Stateless `handle_tool_call`** (1701–1736): a stub kept for the stateless `handle_json_rpc` router; emits `tool-unimplemented` envelopes for every tool — only reachable from the stateless entry point used by tests and `handle_frame`. + - **Envelope/parsing helpers** (1738–2419): `ParamError`, `PathTraversal` (recursive walker for `execution_paths_from`, 1755–1802), `ReferenceDirection`, `required_str` / `required_i64` / `optional_usize` / `optional_bool` / `optional_confidence` argument coercers, envelope builders (`success_envelope`, `tool_error_envelope`, `tool_error_envelope_with_diagnostics`, `success_envelope_with_truncation_and_stats`), `entity_json`, `source_excerpt` + `line_range_excerpt` + `truncate_excerpt`, `inferred_records_from_result` (parses LLM JSON into `InferredCallEdgeRecord`, 2216–2266), `summary_cache_expired` + `timestamp_day_index` + `days_from_civil` (Howard Hinnant civil-from-days algorithm for the 180-day TTL), `caller_json` / `callee_json` / `path_json` / `reference_neighbors`. + - **Unit tests** (2421–2620): 8 tests covering tool-list exact docstrings, initialize result, tools/list wrapping, unknown method/tool/params, frame dispatch round-trip, and multi-frame serve-stdio. +- `src/config.rs` (352 LOC) — `McpConfig` (YAML via `serde_norway`) with `llm` and `integrations.filigree` sections; `LlmConfig` (provider, `enabled`, `allow_live_provider`, `session_token_ceiling: u64` default 1_000_000, `model_id` default `"anthropic/claude-sonnet-4.6"`, `cache_max_age_days` default 180, `max_inferred_edges_per_caller` default 8); `LlmProviderKind::{OpenRouter, Anthropic, Recording}` (with Anthropic actively rejected — `ConfigError::DeprecatedProvider` with code `CLA-CONFIG-DEPRECATED-PROVIDER`, lines 34–43, 169–171); accepts `llm_policy` alias for the `llm` block (line 10, test at 270–284); `select_provider_with_env` (156–191) returns `ProviderSelection::{Disabled, Recording, OpenRouter{api_key_env}}` — opt-in to live OpenRouter is gated by `allow_live_provider` *or* the `CLARION_LLM_LIVE=1` env (173); presence of an API key alone is not enough (test at 287–303); `FiligreeConfig` (127–147) — `enabled` default false, `base_url` default `http://127.0.0.1:8766`, `actor` default `clarion-mcp`, `token_env` default `FILIGREE_API_TOKEN`, `timeout_seconds` default 5. Five unit tests. +- `src/filigree.rs` (238 LOC) — `EntityAssociationsResponse` / `EntityAssociation` (Filigree ADR-029 contract); `FiligreeLookup` trait (45–50); `FiligreeHttpClient` (52–111) — blocking `reqwest::blocking::Client` with `timeout_seconds.max(1)`, returns `Ok(None)` when `enabled=false` (68–70); `associations_for` GETs `{base_url}/api/entity-associations?entity_id={encoded}` with `x-filigree-actor` and optional `Bearer` token; manual percent-encoding restricted to unreserved chars (127–142); three unit tests including a real TCP-server roundtrip (194–237). +- `tests/storage_tools.rs` (1710 LOC) — heavyweight integration tests; 11+ `#[tokio::test]` cases exercising each tool against a seeded SQLite database with `RecordingProvider` LLM substitutes and a stub `FiligreeLookup` (`association` builder at line 573). + +**Dependencies:** + +- Inbound: `clarion-cli` (only — `crates/clarion-cli/src/serve.rs` is the sole consumer of the public API: `McpConfig::from_path`, `select_provider_with_env`, `FiligreeHttpClient::from_config`, `ServerState::new` + builders, `serve_stdio_with_state_on_runtime`). +- Outbound: + - `clarion-core` — `EdgeConfidence`, `INFERRED_CALLS_PROMPT_VERSION`, `InferredCallsPromptInput`, `LEAF_SUMMARY_PROMPT_TEMPLATE_ID`, `LeafSummaryPromptInput`, `LlmProvider`, `LlmProviderError`, `LlmPurpose`, `LlmRequest`, `LlmResponse`, `build_inferred_calls_prompt`, `build_leaf_summary_prompt`; transport `plugin::{ContentLengthCeiling, Frame, TransportError, read_frame, write_frame}` (`lib.rs:11–21`). + - `clarion-storage` — 20 symbols (`lib.rs:22–30`): types `CallEdgeMatch`, `EntityRow`, `InferredCallEdgeRecord`, `InferredEdgeCacheEntry`, `InferredEdgeCacheKey`, `InferredEdgeWriteStats`, `ReaderPool`, `StorageError`, `SummaryCacheEntry`, `SummaryCacheKey`, `UnresolvedCallSiteRow`, `WriterCmd`; functions `call_edges_from`, `call_edges_targeting`, `candidate_entities_for_unresolved_sites`, `child_entity_ids`, `contained_entity_ids`, `entity_at_line`, `entity_by_id`, `find_entities`, `inferred_edge_cache_key_id`, `inferred_edge_cache_lookup`, `normalize_source_path`, `summary_cache_lookup`, `unresolved_call_sites_for_caller`, `unresolved_callers_for_target`. + - External crates: `tokio` (mpsc/oneshot/broadcast, current-thread runtime, `spawn_blocking`), `serde` / `serde_json`, `serde_norway` (YAML), `reqwest::blocking` (Filigree HTTP), `rusqlite` (one direct `prepare` for `reference_neighbors` at line 2378 — the only raw SQL in this crate; everything else routes through `clarion-storage` helpers), `thiserror`. + +**Patterns Observed:** + +- **Read-side dispatch is genuinely thin.** Six of the seven tools (`entity_at`, `find_entity`, `callers_of` non-inferred, `execution_paths_from` non-inferred, `neighborhood` non-inferred, `issues_for`) call a `clarion-storage` helper through `ReaderPool::with_reader`, then envelope the result. Transformation done in `clarion-mcp` is narrow: building tool envelopes (`ok` / `result` / `error` / `diagnostics` / `truncated` / `truncation_reason` / `stats_delta`), shaping `entity_json` / `caller_json` / `callee_json` / `path_json` projections, and the `IssuesForAccumulator` drift classifier. The one substantive in-crate transform is `inferred_records_from_result` (2216–2266) which parses LLM JSON into `InferredCallEdgeRecord` and joins it back against the unresolved-site rows by `site_key`. +- **LLM dispatch lives in this crate, not in `clarion-core`.** `clarion-core` provides prompt templates, the `LlmProvider` trait, and request/response types. The MCP layer owns: cache lookup (`summary_cache_lookup`, `inferred_edge_cache_lookup`), cache-staleness checks (`stale_semantic`, `summary_cache_expired`, ADR-007 five-tuple key in `read_summary_inputs:1010–1016`), the budget ledger (`BudgetReservation` with RAII rollback on drop), the in-flight dispatch coalescer (`inferred_inflight` keyed by `InferredEdgeCacheKey`, 60s timeout), prompt construction, provider invocation (`spawn_blocking` to bridge to the sync provider trait), and the writeback via `WriterCmd::{UpsertSummaryCache, TouchSummaryCache, InsertInferredEdges}`. +- **Filigree integration is genuinely enrich-only.** Three independent skip paths route to `issues_unavailable` (lines 589–594, 619–628), which returns `ok=true` with `available=false` and a `reason` enum (`filigree-disabled` / `filigree-unreachable` / `filigree-client-error` / `entity-not-found`). The other six tools have no Filigree dependency. `FiligreeHttpClient::from_config` returns `Ok(None)` when disabled (filigree.rs:68–70) — disabled is the default. No code path makes a Filigree response required for the tool to succeed; this matches Loom federation §3 (`docs/suite/loom.md`). +- **Confidence-tier opt-in (ADR-028).** `optional_confidence` (1861–1872) defaults to `Resolved`. `inferred` is the only tier that triggers LLM dispatch (via `ensure_inferred_for_target` / `ensure_inferred_for_caller`). `ambiguous` is read-only over existing static-edge rows. +- **Writer-actor handoff.** All mutating storage operations go through `mpsc::Sender` + a `oneshot::Sender>` ack (`send_writer`, 1157–1171). Translates `WriterGone` / `WriterNoResponse` storage errors into retryable tool envelopes. ADR-011 compliance. +- **Stateful and stateless entry points co-exist.** The stateless `handle_json_rpc` (line 154) + `handle_tool_call` (line 1701) pair always emits `tool-unimplemented` envelopes for every tool; the stateful `ServerState::handle_json_rpc` (line 228) is the real dispatcher. The stateless path remains usable for `initialize` / `tools/list` and is exercised by unit tests inside the file. +- **Truncation contract** — every list-shaped success envelope can carry `truncation_reason: "edge-cap" | "issue-cap" | "entity-cap"`. `execution_paths_from` enforces `execution_edge_cap` (default 500); `issues_for` enforces a hardcoded 100-issue cap (line 631) and a 1000-contained-entity cap (`read_issues_for_entities:655`). +- **Time normalisation as plain math.** No `chrono` / `time` dependency — `default_now_string` emits `unix:{seconds}`, `timestamp_day_index` accepts either `unix:N` or ISO `YYYY-MM-DD…` prefix, and `days_from_civil` is the Howard Hinnant algorithm inline (2306–2314). + +### Tool table + +| Tool | Required inputs | Optional inputs | Primary storage helper | LLM dispatch path | +|------|------------------|------------------|-------------------------|--------------------| +| `entity_at` | `file: string`, `line: int ≥ 1` | — | `entity_at_line` (after `normalize_source_path`) | No | +| `find_entity` | `pattern: string` | `limit: 1..=100` (default 20), `cursor: string\|null` (numeric offset) | `find_entities` | No | +| `callers_of` | `id: string` | `confidence: resolved\|ambiguous\|inferred` (default `resolved`) | `call_edges_targeting` + `entity_by_id` | Only when `confidence=inferred` → `ensure_inferred_for_target` | +| `execution_paths_from` | `id: string` | `max_depth: 1..=8` (default 3), `confidence` (default `resolved`) | `call_edges_from` + `PathTraversal` (resolved/ambiguous) or `inferred_execution_paths` (inferred) | Only when `confidence=inferred` → bounded BFS of `ensure_inferred_for_caller` per node | +| `summary` | `id: string` | — | `summary_cache_lookup` then `WriterCmd::TouchSummaryCache` / `UpsertSummaryCache` | **Yes** — leaf-scope (ADR-030), `LlmPurpose::Summary`, max_output_tokens 512 | +| `issues_for` | `id: string` | `include_contained: bool` (default true) | `entity_by_id` + `contained_entity_ids` (cap 1000) | No — Filigree HTTP per entity via `spawn_blocking` | +| `neighborhood` | `id: string` | `confidence` (default `resolved`) | `entity_by_id` + `call_edges_targeting` + `call_edges_from` + `child_entity_ids` + `reference_neighbors` | Only when `confidence=inferred` → both `ensure_inferred_for_target` *and* `ensure_inferred_for_caller` (lines 528–534) | + +### LLM cache-key dispatch table + +| Path | Cache key tuple (ADR-007) | Source line | +|------|----------------------------|-------------| +| Summary | `entity_id` + `content_hash` + `prompt_template_id = LEAF_SUMMARY_PROMPT_TEMPLATE_ID` + `model_tier` (from `LlmProvider::tier_to_model("summary")`) + `guidance_fingerprint = "guidance-empty"` | `lib.rs:1010–1016` | +| Inferred edges | `caller_entity_id` + `caller_content_hash` + `model_id` (from `tier_to_model("inferred_edges")`) + `prompt_version = INFERRED_CALLS_PROMPT_VERSION` | `lib.rs:816–821` | + +On miss, both paths reserve via `BudgetLedger` (token-pessimistic, ceiling default 1_000_000 input+output combined), invoke the provider on `spawn_blocking`, commit actual tokens (or flip `blocked=true`), and on success write back via the writer-actor. Subsequent dispatches for the same key short-circuit through the in-flight coalescer (`coalesced_inferred_dispatch`, 865–908) which `broadcast::subscribe`s and waits up to 60 s. + +**Concerns:** + +- **`lib.rs` is 2620 LOC in one file.** Discovery question #1 — internal structure is *coherent* (clear bands: protocol surface → `ServerState` → per-tool handlers → LLM pipelines → transport loop → helpers), but the file is large enough to warrant subdivision on size grounds alone. The `IssuesForAccumulator`, the LLM inferred-edges pipeline (719–995), the LLM summary pipeline (997–1155), the budget ledger (1180–1316), and the envelope/projection helpers (1874–2400) are each plausible standalone modules. The current single-file layout is not a god-file in the architectural sense — each band has a single responsibility — but the size will degrade code-review velocity and grep ergonomics. +- **Dead stateless `handle_tool_call` stub** (`lib.rs:1701–1736`): emits `tool-unimplemented` envelopes for every tool name. Reachable only via the stateless `handle_json_rpc` (154) and `handle_frame` (1621) paths. `handle_frame` is exercised by one unit test (2542–2560) and is exported from the crate, so any external consumer that wires the stateless path will get permanently-broken `tools/call` responses. Not a runtime defect inside the CLI (which uses `handle_frame_with_state`), but a footgun in the public API. +- **`reference_neighbors` (lib.rs:2363–2400)** issues raw SQL against the `edges` table directly, bypassing the `clarion-storage` helper layer. It is the *only* place in this crate that does so. This creates a hidden coupling to the `edges` schema (`kind = 'references'`, `confidence`, `source_byte_start`, `source_byte_end`) outside the storage crate. If the schema changes, `clarion-storage` callers and tests will catch it but this function will not. +- **`InferredCallsResponseEdge::confidence: Option` field is parsed but unused for envelope shape** (lib.rs:1601–1607, used in 2247–2255). The model's reported confidence is stored as a property in the inferred-edge row's `properties_json`, but the storage layer does not surface it back through `caller_json`/`callee_json` — the tool envelope only exposes `edge_confidence` (the tier: resolved/ambiguous/inferred). The model's per-edge confidence is therefore preserved on disk but not queryable; consumers needing the score must hand-parse `properties_json`. +- **Coalesced-dispatch waiters get a generic stats delta when the leader fails.** `InferredDispatchOutcome::from_result` (1574–1595, used at 902–908) broadcasts a clonable outcome; non-leader waiters that receive a failure outcome surface it as their own (line 884–887). Acceptable, but the leader's diagnostics (e.g. `CLA-LLM-INVALID-JSON` usage block) are visible to the leader only; waiters see the failure code/message but lose the per-response diagnostics array. Minor observability gap. +- **`source_excerpt` (lib.rs:2151)** uses `std::fs::read_to_string` on the *current on-disk file path* to build LLM prompt input. This is *not* the content hash that keyed the cache; the file may have changed between the time the entity was scanned and the time the tool runs. The cache key still uses the stored `content_hash`, so a stale read here produces a cache miss with a fresh-but-misaligned prompt. The `stale_semantic` flag covers structural drift (caller_count / fan_out) but not source-text drift. Documented as a known v0.1 trade-off in the surrounding code? — no comment found. +- **`BudgetLedger::blocked` is sticky for the lifetime of the `ServerState`**: once any reservation overshoots, `blocked` flips to `true` (1196, 1296) and every subsequent LLM tool returns `token-ceiling-exceeded` until process restart. No reset path; no way to lift the ceiling without dropping the state. Matches a session-token semantic but is undocumented in the public API. +- **`FiligreeConfig::actor` blank handling**: `FiligreeHttpClient::associations_for` only sets the `x-filigree-actor` header when the actor string is non-blank (filigree.rs:94–96); Filigree currently requires the header for some endpoints. Silent omission rather than rejection at config-load. +- **No `Drop` cleanup for in-flight broadcast senders on leader cancellation.** If the leader task panics or is dropped *before* reaching the explicit `remove` at line 904, the `inferred_inflight` entry leaks until the next dispatch for the same key. `broadcast::Sender` itself is not a resource leak, but the map entry blocks subsequent dispatches from claiming leadership; subsequent callers will subscribe to a now-dead sender and time out at 60 s. Low-probability but present. + +### Confidence Assessment + +**Confidence:** High — Read 100% of `config.rs` (352 lines), 100% of `filigree.rs` (238 lines), 100% of the `lib.rs` declarations/dispatch (1–1700) and the helper/test bands (1700–2620). Sampled five handler bodies in full (`tool_entity_at`, `tool_find_entity`, `tool_callers_of`, `inferred_execution_paths`, `tool_issues_for`, `tool_summary`) and the LLM pipelines (`ensure_inferred_for_caller` through `perform_inferred_dispatch`). Cross-verified inbound dependency by reading `clarion-cli/src/serve.rs` (137 lines). Cross-verified outbound dependency claims against the `use` block at `lib.rs:11–34`. Cross-verified ADR alignment by quoting cache-key construction sites (5-tuple at 1010–1016, 4-tuple at 816–821) and ADR-028 default in `optional_confidence` (1864). + +### Risk Assessment + +- **Size-induced review burden** (lib.rs 2620 LOC) — Medium operational risk; not a correctness risk. The internal banding makes incremental refactors safe. +- **Dead stateless `handle_tool_call` stub in public API surface** — Low surface but high blast radius for any external consumer. Single fix: either remove from public exports or make it forward to the same handlers as the stateful path. +- **`reference_neighbors` raw SQL** — Schema-coupling risk; would not be caught by `clarion-storage` integration tests. +- **`source_excerpt` reads live disk, not the hashed snapshot** — Correctness drift risk under concurrent file modification; affects prompt fidelity but not cache correctness. +- **Sticky budget ledger** — Operational risk: process restart required after one ceiling breach. Acceptable for v0.1 / session semantics. +- **Filigree enrich-only contract** — Verified clean. Discovery question #5 answered: no Filigree code path is load-bearing. + +### Information Gaps + +- The Sprint-2 e2e script `tests/e2e/sprint_2_mcp_surface.sh` was not read in this pass (out of scope per task framing); coverage of the seven tools end-to-end is documented as "presumed" in `01-discovery-findings.md:138`. +- The integration tests at `tests/storage_tools.rs` (1710 LOC) were enumerated but not read in full; the `RecordingProvider` plumbing and the `state_for_filigree` stub were sampled to confirm they exist (lines 244–252). +- ADR text for ADR-007/028/029/030 was not re-opened in this pass; alignment claims rely on the cache-key/confidence-tier code matching the documented intent paraphrased in the task brief. +- The model's per-edge `confidence: Option` field is parsed from LLM output but not surfaced in tool responses — whether this is intentional (ADR-028 tiers are coarse-grained on purpose) or a documentation gap was not verified against the ADR. + +### Caveats + +- The "thin dispatch" characterisation is true for the six read-only tools but does not apply to the LLM-dispatch paths (`tool_summary` plus the `confidence=inferred` branches of `callers_of` / `execution_paths_from` / `neighborhood`), which carry substantive in-crate logic: cache-key construction (ADR-007), budget reservation, in-flight coalescing, prompt construction via `clarion-core` helpers, provider invocation on `spawn_blocking`, JSON-shape validation, and writeback via the writer-actor. +- The LOC band offsets cited in the catalog were computed from the on-disk `lib.rs` and are stable against the working tree at the time of analysis; minor drift (the file grew by 171 lines during B.8 per `01-discovery-findings.md:323`) means line numbers in this section are post-B.8. +- "MCP protocol revision `2025-11-25`" is sourced from the in-code constant (`lib.rs:36`); whether that matches the upstream MCP spec revision identifier was not independently verified. +- The Filigree HTTP client uses `reqwest::blocking` despite living in an otherwise async crate — calls are wrapped in `tokio::task::spawn_blocking` at `lib.rs:613`. Not a defect, but worth flagging if the crate is ever migrated to an async Filigree client. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-storage.md b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-storage.md new file mode 100644 index 00000000..68bf215e --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/section-clarion-storage.md @@ -0,0 +1,149 @@ +## clarion-storage + +**Location:** `crates/clarion-storage/` + +**Responsibility:** Persists Clarion's entity/edge graph, run provenance, and LLM caches in a single SQLite database under `.clarion/clarion.db`. All mutations funnel through a single writer-actor task (sole `rusqlite::Connection`); all reads come from a `deadpool-sqlite` pool. The crate also owns the schema migration runner, the PRAGMA discipline, the edge-contract validator, and the typed query helpers consumed by `clarion-mcp` and `clarion-cli`. + +### Internal structure + +**Module roster** (`src/lib.rs:7–15`, all `pub mod`): + +| Module | LOC | Role | +|---|---|---| +| `writer.rs` | 817 | Writer-actor: spawn, command loop, edge-contract enforcement, per-N batch commits, parent/contains consistency check at `CommitRun` | +| `query.rs` | 569 | Read-side helpers (graph navigation, FTS-or-LIKE search, unresolved call-site fan-out) | +| `cache.rs` | 251 | `SummaryCacheKey` (5-tuple per ADR-007) + `InferredEdgeCacheKey` (4-tuple) and their upsert/lookup/touch helpers | +| `commands.rs` | 183 | `WriterCmd` enum (9 variants) + POD records + `RunStatus` | +| `schema.rs` | 118 | Embed-and-apply migration runner (`include_str!` of the single `.sql` file) | +| `reader.rs` | 88 | `ReaderPool` wrapper around `deadpool-sqlite::Pool` | +| `unresolved.rs` | 50 | Replace-by-caller bookkeeping for unresolved call sites | +| `error.rs` | 48 | `StorageError` taxonomy (11 variants, `thiserror`) | +| `pragma.rs` | 45 | WAL/synchronous=NORMAL/busy_timeout=5000/foreign_keys=ON discipline | +| `lib.rs` | 35 | Curated `pub use` facade | + +**Schema (ER summary)** — single migration `migrations/0001_initial_schema.sql` (289 LOC). Eight base tables, one FTS5 virtual table, three triggers, one view, two generated columns: + +``` + ┌─────────────────────────────────────────────┐ + │ entities (PK id TEXT) │ + │ + virtual cols scope_level / scope_rank │ + │ + indexes on kind, plugin_id, parent_id, │ + │ source_file_id, source_file_path, │ + │ content_hash, last_seen_commit, │ + │ scope_rank (partial), git_churn (partial)│ + └──┬──────────────────┬────────┬─────────────┘ + │self-ref │FK FK │FK + parent_id │ source_file_id │ │ + ▼ ▼ ▼ + ┌──────────────┐ ┌──────────────────────────────────────┐ + │ entity_tags │ │ edges WITHOUT ROWID │ + │ (entity_id, │ │ PK (kind, from_id, to_id) │ + │ tag) PK │ │ CHECK confidence IN │ + │ ON DELETE │ │ (resolved, ambiguous, inferred) │ + │ CASCADE │ │ FKs: from_id, to_id, source_file_id │ + └──────────────┘ │ ALL ON DELETE CASCADE │ + └──────────────────────────────────────┘ + ▲ ▲ + │entity_id FK │caller_entity_id FK + ┌─────────────────────┐ ┌────────────────────────────────┐ + │ findings (PK id) │ │ entity_unresolved_call_sites │ + │ CHECK kind ∈ 5 │ │ PK (caller_entity_id, │ + │ CHECK severity ∈ 5 │ │ caller_content_hash, │ + │ CHECK status ∈ 4 │ │ site_key) │ + │ FK entity_id │ └────────────────────────────────┘ + └─────────────────────┘ + ▲caller_entity_id FK + ┌────────────────────────────┐ ┌──────────────────────────┐ + │ inferred_edge_cache │ │ summary_cache │ + │ PK (caller_entity_id, │ │ PK 5-tuple (entity_id, │ + │ caller_content_hash, │ │ content_hash, │ + │ model_id, │ │ prompt_template_id, │ + │ prompt_version) │ │ model_tier, │ + │ FK caller_entity_id │ │ guidance_fingerprint)│ + └────────────────────────────┘ │ CHECK stale_semantic∈(0,1)│ + └──────────────────────────┘ + + ┌──────────────────────────┐ ┌────────────────────────────┐ + │ runs (PK id) │ │ schema_migrations │ + │ CHECK status ∈ (running, │ │ (version PK, name, │ + │ skipped_no_plugins, │ │ applied_at) │ + │ completed, failed) │ └────────────────────────────┘ + └──────────────────────────┘ + + FTS5 virtual: entity_fts (entity_id UNINDEXED, name, short_name, + summary_text, content_text); kept in sync by triggers + entities_ai / entities_au / entities_ad. + + View: guidance_sheets — projects entities WHERE kind='guidance' + with json_extract of `properties` + json_group_array of tags. +``` + +ADR-031 `CHECK` discipline (lines 89, 107–112, 124–125, 153, 200–201): closed core-owned vocabularies receive `CHECK` clauses (`edges.confidence`, `findings.{kind, severity, status}`, `summary_cache.stale_semantic`, `runs.status`). Plugin-extensible vocabularies deliberately omit `CHECK` per ADR-022 — `entities.kind` (`migrations/0001_initial_schema.sql:33–36`) and `edges.kind` (`migrations/0001_initial_schema.sql:77–81`); enforcement at those columns is the writer-actor (`writer.rs::enforce_edge_contract` for edges, manifest acceptance for entity kinds). + +**Writer-actor command set** (`commands.rs::WriterCmd`, 9 variants): + +| Variant | Lifecycle | Notes | +|---|---|---| +| `BeginRun` | analyze-time | `runs` INSERT with `status='running'`, opens `BEGIN` (`writer.rs:308–330`) | +| `InsertEntity` | analyze-time | Single INSERT into `entities`; counts toward batch boundary (`writer.rs:332–390`) | +| `InsertEdge` | analyze-time | Calls `enforce_edge_contract` (`writer.rs:411–472`) then `INSERT OR IGNORE`; dedupe increments `dropped_edges_total`, ambiguous accepts bump `ambiguous_edges_total` (`writer.rs:474–520`) | +| `InsertInferredEdges` | query-time (MCP) | Upserts inferred-edge cache row, GCs stale inferred edges for the caller, inserts new ones; refuses to shadow static resolved/ambiguous calls (`writer.rs:522–599`) | +| `UpsertSummaryCache` | query-time (MCP) | 5-tuple upsert on `summary_cache` (`cache.rs:48–85`) | +| `TouchSummaryCache` | query-time (MCP) | `UPDATE summary_cache SET last_accessed_at` (`cache.rs:112–132`) | +| `ReplaceUnresolvedCallSitesForCaller` | analyze-time | Delete-then-insert pattern; replaces all sites for one caller atomically inside the run transaction (`writer.rs:601–621`, `unresolved.rs:20–50`) | +| `CommitRun` | analyze-time | Runs the B.3 parent/contains dual-encoding check **inside** the open transaction (`writer.rs:733–796`); on mismatch rolls back the run's writes and marks `runs.status='failed'` with `CLA-INFRA-PARENT-CONTAINS-MISMATCH` in `stats.failure_reason`; on success folds the `runs` UPDATE into the final COMMIT (`writer.rs:671–727`) | +| `FailRun` | analyze-time | ROLLBACK + `UPDATE runs SET status='failed'` (`writer.rs:798–817`) | + +The actor multiplexes analyze-time and query-time mutations on the same connection. `query_time_write` (`writer.rs:647–669`) commits any open analyze-time batch, runs the MCP write, and reopens a `BEGIN` if a run is still active — so analyze-time and MCP traffic cannot deadlock or interleave on the same transaction. Batch cadence is `DEFAULT_BATCH_SIZE = 50` writes (`writer.rs:35`, `bump_writes_and_maybe_commit` at `writer.rs:628–645`); the `INSERT OR IGNORE` edge dedupe is workload-shape-invariant because UNIQUE conflicts still bump the batch counter. + +Channel-closed cleanup (`writer.rs:251–273`): if the `Writer` is dropped mid-run, the actor self-heals by issuing `ROLLBACK` and marking the surviving run row `failed` with `failure_reason="writer channel closed unexpectedly"`. This is the durability backstop for the supervisor in `clarion-cli::analyze`. + +**Edge contract** (`writer.rs::enforce_edge_contract`, line 411). Ontology is hard-coded as `STRUCTURAL_EDGE_KINDS = ["contains", "in_subsystem", "guides", "emits_finding"]` (`writer.rs:394`) and `ANCHORED_EDGE_KINDS = ["calls", "references", "imports", "decorates", "inherits_from"]` (`writer.rs:395–401`) — nine kinds total per ADR-026/028. Structural edges MUST have `confidence=resolved` and NULL `source_byte_*`; anchored edges MUST have both `source_byte_*` set, and may NOT be `inferred` at scan time (`writer.rs:440–449`) because inferred-tier edges are query-time-only. Violations return `StorageError::WriterProtocol` with one of three CLA codes (`CLA-INFRA-EDGE-CONFIDENCE-CONTRACT`, `CLA-INFRA-EDGE-SOURCE-RANGE-CONTRACT`, `CLA-INFRA-EDGE-UNKNOWN-KIND`) so the surrounding `runs.stats.failure_reason` carries the code (`writer.rs:402–410`). + +**Reader pool** (`reader.rs`). `ReaderPool::open` builds a `deadpool_sqlite::Pool` with `Runtime::Tokio1` and a caller-supplied `max_size` (the CLI passes its own value; tests use small caps). `with_reader` acquires from the pool, submits a `'static` closure to deadpool's `interact()` blocking task pool, and applies read-side PRAGMAs (`busy_timeout=5000`, `foreign_keys=ON`) on every acquisition. Retry-on-`SQLITE_BUSY` is delegated to SQLite itself via `busy_timeout` rather than an application-level loop — both writer and readers wait up to 5 s for the lock. WAL mode (set on the writer's first connection, `pragma.rs:16–31`) is what lets readers proceed concurrently without seeing in-flight writes. `waiting_count()` (`reader.rs:85–87`) is exposed `#[doc(hidden)]` for deterministic test polling. + +**Cache keys.** `SummaryCacheKey` (`cache.rs:7–14`) materialises ADR-007's 5-tuple exactly: `(entity_id, content_hash, prompt_template_id, model_tier, guidance_fingerprint)`. `ontology_version` is *not* in the key (correct per ADR-007 — that field is handshake validation only). `InferredEdgeCacheKey` (`cache.rs:30–36`) is a 4-tuple `(caller_entity_id, caller_content_hash, model_id, prompt_version)`. **Boundary clarification**: cache lookup/upsert helpers in `cache.rs` are pure storage operations; on a miss, `clarion-mcp::lib.rs` decides whether to call the LLM (via `clarion-core::LlmProvider`), then enqueues the result via `WriterCmd::UpsertSummaryCache` or `WriterCmd::InsertInferredEdges`. This crate does not depend on `clarion-core::LlmProvider`; its only `clarion-core` dependency is `EdgeConfidence` (`commands.rs:14`, `query.rs:6`). + +**Query helpers re-exported via `lib.rs`** (`lib.rs:27–32`): `entity_by_id`, `entity_at_line` (innermost-entity-at-line with tie-break by source-range size then kind preference function→class→module), `find_entities` (FTS5 if the pattern is alnum/underscore; LIKE-with-escape otherwise — see `is_fts_safe` at `query.rs:552`), `call_edges_from` / `call_edges_targeting` (apply ADR-028 confidence ceiling; for `ambiguous` edges, expand the `properties.candidates[]` JSON array into multiple match rows — `query.rs:218–235`, `523–534`), `contained_entity_ids` (iterative DFS over `contains` edges with cycle guard and `max_entities` truncation — `query.rs:354–388`), `unresolved_call_sites_for_caller`, `unresolved_callers_for_target` (LIKE-suffix match on `callee_expr` with same-file preference — `query.rs:294–332`), `candidate_entities_for_unresolved_sites`, `child_entity_ids`, `normalize_source_path` (project-root jail; both lexical normalisation and `canonicalize()` are checked — `query.rs:76–104`). + +### External interface + +`lib.rs` (35 LOC) re-exports a closed surface: the `WriterCmd`/`EdgeRecord`/`EntityRecord`/`RunStatus` typed boundary; `Writer` and the two channel/batch constants; `ReaderPool`; the query helpers; the cache key types and their three pure helpers (`summary_cache_lookup`, `inferred_edge_cache_lookup`, `inferred_edge_cache_key_id`); `StorageError`/`Result`. Internal modules `pragma` and `schema` are `pub mod`, used by `clarion-cli::install` (`crates/clarion-cli/src/install.rs:20`). `clarion-mcp::lib.rs:22–30` consumes 18 named symbols; `clarion-cli::analyze.rs:24–27` consumes 4 (writer/command shapes only). + +### Dependencies + +- **Inbound** (verified via `use clarion_storage::` grep): + - `clarion-mcp` — full read surface + the four query-time `WriterCmd` variants + - `clarion-cli` — `analyze.rs` (writer + commands), `install.rs` (`pragma` + `schema`), `serve.rs` (`Writer` + `ReaderPool` + batch constants) +- **Outbound** (`Cargo.toml`): + - `clarion-core` — only for `EdgeConfidence` (used in `commands.rs` + `query.rs`); intentionally minimal + - `deadpool-sqlite 0.8` — async-friendly read pool (ADR-011) + - `rusqlite 0.31` — bundled SQLite, sole write driver + - `tokio` — `mpsc` + `oneshot` channels, `spawn_blocking` for the writer task + - `serde_json` — JSON shape validation on `InferredCallEdgeRecord.properties_json` + `ambiguous` `candidates[]` decoding + - `thiserror`, `tracing` + +No outbound dependency on `clarion-mcp`, `clarion-cli`, or any plugin crate. Crate-level acyclicity holds. + +### Patterns observed + +- **Actor + pool split (ADR-011).** Single writer task owns the write connection; all multi-row mutations are batched into a transaction sized by writes (entity inserts + edge insert attempts, including dedupes). The pattern is documented as L3 lock-in (`writer.rs:1–13`). +- **Typed command boundary.** Every mutation is a `WriterCmd` variant carrying its own `oneshot::Sender>` ack — per-command response, no batched fan-in. Adding a new mutation is a single-file append (`commands.rs`) plus a match arm (`writer.rs:152–249`). +- **Defence in depth on closed vocabularies (ADR-031).** Two enforcement layers: the writer-actor (canonical) and SQL `CHECK` (backstop). The migration's per-column comments name which ADR closes each vocabulary; plugin-extensible columns are explicitly tagged "no CHECK by policy." +- **Edge-contract failure codes are findings.** When `enforce_edge_contract` rejects, the error message embeds `CLA-INFRA-EDGE-*` codes that surface in `runs.stats.failure_reason` — making writer-rejected edges observable as machine-greppable findings rather than opaque protocol errors. +- **`query_time_write` interleaves cleanly.** Query-time MCP writes commit the analyze-batch first, then reopen `BEGIN` if a run is still in progress — the actor never holds an MCP cache row open inside an analyze transaction. +- **Validation depth on path inputs.** `normalize_source_path` does lexical normalisation *and* `canonicalize()`, and checks containment against the canonicalized project root in both forms (`query.rs:76–104`). Prevents symlink/`..` escape against `entity_at_line` and `find_entity`. +- **B.3 dual-encoding check at commit.** Parent/contains consistency is verified inside the transaction at `CommitRun` time (`writer.rs:733–796`), so an inconsistent run rolls back rather than persisting a half-corrupt graph. + +### Concerns + +- **Single migration, edit-in-place under ADR-024.** `migrations/0001_initial_schema.sql` has been edited three times (initial; 2026-05-03 ADR-024 vocabulary rename; 2026-05-18 ADR-031 `CHECK` clauses). The retirement trigger is documented in-file (`0001_initial_schema.sql:10–16`) but no automated check fires when the trigger condition (external operator builds `.clarion/clarion.db` from a published Clarion build) is met. Manual discipline only. Mitigated by the migration's own `schema_migrations` row idempotence (`schema.rs:81–89`). +- **Edge ontology is duplicated.** `STRUCTURAL_EDGE_KINDS` + `ANCHORED_EDGE_KINDS` are hard-coded in `writer.rs:394–401`; ADR-026/028 are the design source; the Python plugin's manifest declares `edge_kinds = ["contains", "calls", "references"]` independently. A new kind requires edits in at least three places (manifest, writer, ADR). No compile-time enforcement that these stay in sync. +- **Schema-shape FK in `entities.source_file_id` is self-referential** (`migrations/0001_initial_schema.sql:40`). Works because source-file entities are inserted before their contained functions/classes (plugin traversal order), but there is no constraint that enforces insertion order. A plugin emitting children before parents would fail with an FK violation, surfacing as an opaque `rusqlite::Error` rather than a writer-protocol error. +- **`busy_timeout=5000` is the only `SQLITE_BUSY` mitigation.** Under heavy contention a reader can fail with a SQLite-level busy error rather than being retried at the application layer. The B.8 scale test exercises this path in practice; no per-attempt retry loop exists in `with_reader`. +- **`InsertEdge` and `InsertEntity` share a single batch counter.** An edge-heavy file (e.g., a module with many `references` edges) can flush the batch boundary mid-file. Documented behaviour (`writer.rs:285–289`) but worth flagging — long transactions are not bounded by file boundary. +- **No write-side throttling on `WriterCmd` channel.** `DEFAULT_CHANNEL_CAPACITY = 256` (`writer.rs:38`); a faster producer than the actor will block via `Sender::send().await` backpressure, which is correct, but no metric is exposed for "time spent blocked on writer queue." + +### Confidence + +**Confidence:** High — Read 100% of every `src/*.rs` module (10 files, 1 950 LOC) and the migration in full (289 LOC). Cross-validated dependency direction by grepping `use clarion_storage::` across the workspace: only `clarion-mcp` and `clarion-cli` consume it; no inbound cycles. Confirmed `WriterCmd` variant count (9) matches the actor's match arms one-to-one. Schema CHECK constraints verified at exact line numbers against ADR-031's "closed vs. extensible" decision. Edge-contract code-paths (`enforce_edge_contract` and the three CLA codes it emits) read end-to-end. ADR cross-references are inline in both the migration and the writer source, so the "ADR says X / code does Y" gap is small. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/section-fixture-plugin.md b/docs/arch-analysis-2026-05-18-1244/temp/section-fixture-plugin.md new file mode 100644 index 00000000..96688133 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/section-fixture-plugin.md @@ -0,0 +1,53 @@ +## Test-only Rust fixture plugin (`clarion-plugin-fixture`) + +**Location:** `crates/clarion-plugin-fixture/src/` + +**Responsibility:** Protocol-compatible stand-in for a real language plugin: a minimal Rust binary speaking the same Content-Length-framed JSON-RPC 2.0 protocol on stdin/stdout as the Python plugin, used by `clarion-core`'s `host_subprocess` integration test to exercise `PluginHost::spawn` end-to-end without bringing a Python interpreter and pyright into the test loop. + +**Key Components:** + +- `Cargo.toml` (19 lines) — declares a single `[[bin]]` target (`clarion-plugin-fixture`, `src/main.rs`); depends on `clarion-core` (path dep, version `0.1.0-dev`) and `serde_json` from the workspace; inherits workspace `[lints]`. No library is published. +- `src/main.rs` (128 lines, full code) — the entire plugin. One blocking `loop` over `read_frame(&mut reader, ContentLengthCeiling::DEFAULT)` (`main.rs:33`); per-frame `serde_json::from_slice` to a free-form `Value` so it can branch on `id`-presence (notification vs. request) before typed deserialisation (`main.rs:37-46`). Five method branches matching the L4 protocol surface: + - `initialize` (request) → `InitializeResult { name: "clarion-plugin-fixture", version: "0.1.0", ontology_version: "0.1.0", capabilities: {} }` (`main.rs:68-76`). + - `initialized` (notification) → state transition only, no reply (`main.rs:50-53`). + - `analyze_file` (request) → extracts `params.file_path` (or `""`), echoes it back inside one stub entity `{"id": "fixture:widget:demo.sample", "kind": "widget", "qualified_name": "demo.sample", "source": {"file_path": }}`, returns `AnalyzeFileResult { entities: vec![entity], edges: vec![], stats: default }` (`main.rs:77-108`). + - `shutdown` (request) → empty `ShutdownResult` (`main.rs:109-112`). + - `exit` (notification) → `std::process::exit(0)` (`main.rs:54-56`). +- `src/lib.rs` (3 lines) — comment-only stub explaining the crate is binary-only; exists so Cargo resolves the workspace member cleanly. + +**Dependencies:** + +- Inbound: `crates/clarion-core/tests/host_subprocess.rs` is the sole consumer — it locates the binary via `CARGO_BIN_EXE_clarion-plugin-fixture`, falling back to `/{debug,release}/clarion-plugin-fixture`; the manifest `tests/fixtures/plugin.toml` is `include_bytes!`-embedded at compile time (`host_subprocess.rs:16`). CI's `walking-skeleton` job builds this binary as part of `cargo build --workspace --bins` so the test can find it on disk (see `CLAUDE.md` build-commands section: "wp2_e2e tests need clarion-plugin-fixture on disk"). +- Outbound: `clarion-core::plugin::limits::ContentLengthCeiling` (the 8 MiB default), `clarion-core::plugin::transport::{Frame, read_frame, write_frame}` (the shared framing codec), `clarion-core::plugin::{AnalyzeFileParams, AnalyzeFileResult, AnalyzeFileStats, InitializeResult, JsonRpcVersion, ResponseEnvelope, ResponsePayload, ShutdownResult}` (the typed protocol structs); `serde_json` for the free-form `Value` pre-dispatch. + +**Patterns Observed:** + +- **Protocol-by-shared-types.** The fixture reuses `clarion-core`'s own protocol structs (`InitializeResult`, `AnalyzeFileResult`, `ResponseEnvelope`, …) for response serialisation — there is no parallel schema definition. A breaking change to `protocol.rs` therefore fails compilation of the fixture, not at runtime under test, which is the right ordering. +- **Same ceiling as production.** Frame reads use `ContentLengthCeiling::DEFAULT` (the ADR-021 §2b 8 MiB cap), with the source comment explicitly noting that `unbounded()` is now `#[cfg(test)]`-only (`main.rs:30-32`). The fixture lives under the same wire-cap discipline as a real plugin. +- **Fail-fast on protocol violations.** Every recoverable branch in a real plugin is `std::process::exit(1)` here — malformed frame, non-object body, missing/non-string `method`, integer-id parse failure, unknown method, params-deserialise failure (`main.rs:34, 39, 45, 57, 64, 90, 113`). Acceptable because the consumer is exclusively an integration test; the alternative would obscure protocol-violation bugs behind fixture-side error handling. +- **Notification vs. request branching on `id`-presence.** Reads the raw `Value` first, checks `id.is_some_and(|v| !v.is_null())` to decide whether the frame requires a response (`main.rs:42, 48-60`). This matches the JSON-RPC 2.0 spec and parallels the Python plugin's branching in `server.dispatch` (`server.py:239-261`). +- **Stable identity for assertions.** `plugin_id = "fixture"`, kind `"widget"`, and the literal entity ID `"fixture:widget:demo.sample"` are baked into the source — `host_subprocess.rs` asserts on this exact string, so the test signal is exact-match rather than parse-and-inspect. + +**Concerns:** + +- **No request-id sanity on `shutdown`.** Unlike the Python plugin, the fixture doesn't gate `analyze_file` on having received `initialized` — `state.initialized` doesn't exist. This is fine for the single happy-path test it supports, but means the fixture cannot exercise the host's `-32002 NOT_INITIALIZED` error path. If a future test wanted to assert that the host *itself* sequences the handshake correctly, it would have to verify host-side state rather than fixture-side rejection. +- **`exit(1)` on any malformed frame is observable only as a non-zero process exit.** The host-side test gets no structured signal about which branch failed. For an integration test fixture this is by design; flagging because anyone running the fixture by hand against a non-test client will see opaque exits. +- **No stderr discipline.** A real plugin (Python's `stdout_guard.py`) reserves stdout strictly for framing; the fixture relies on the absence of any `eprintln!` or `println!` in its own code rather than installing a guard. For a 128-line file with `serde_json` as the only output-side dep this is fine, but worth noting as a delta from the production-plugin pattern. + +**Confidence:** High — Read `main.rs` (128 lines, 100% of file), `lib.rs` (3 lines, 100%), `Cargo.toml` (19 lines, 100%); cross-verified consumer via `crates/clarion-core/tests/host_subprocess.rs` lines 3-7, 15-27, and 60-66 (binary-location strategy, fixture identity assertions, manifest constants). Cross-validated against `docs/arch-analysis-2026-05-18-1244/01-discovery-findings.md` §4 Subsystem E framing and `CLAUDE.md` layout summary. Protocol identity confirmed by the matching set of imports from `clarion_core::plugin::*` against the Python plugin's `server.py:7-19` docstring describing the same five methods and response shapes. Content-Length framing parity confirmed via the explicit `ContentLengthCeiling::DEFAULT` (8 MiB) source comment matching the Python `MAX_CONTENT_LENGTH = 8 * 1024 * 1024` at `server.py:48`. + +**Information Gaps:** + +- Did not read the upstream `clarion_core::plugin::transport` module to verify exactly how `read_frame` / `write_frame` interpret the ceiling; took the source comment at face value. +- Did not run `cargo build -p clarion-plugin-fixture` on the current branch to confirm the binary still compiles. Treated the unmodified `Cargo.toml` and the recent (b87bc1d) signoff record as sufficient evidence that the walking-skeleton CI job was green at sprint close. + +**Caveats:** + +- "Protocol-compat" here means *exact wire-shape compatibility* on the five L4 methods. The fixture does not exercise the `capabilities.wardline` probe shape, `parse_status` on module entities, `parent_id`/`contains` edges, calls/references resolution, the `stats` payload's `unresolved_call_sites`, or any of the Sprint-2 ontology surface. It is a *minimum*-shape test stand-in, not a feature-parity one. +- The fixture's `ontology_version = "0.1.0"` (`main.rs:72`) is deliberately the Sprint-1 baseline; this is the version against which the host's manifest-handshake validator is tested. It does *not* track the Python plugin's `0.5.0` and shouldn't. + +**Risk Assessment:** + +- *Drift between fixture and real plugins.* The fixture has been stable since Sprint 1 close and the protocol contract is enforced by shared `clarion-core` types, so the drift surface is bounded to behavioural-not-structural divergence (e.g. a real plugin adding handshake side-effects the fixture doesn't model). The host-side test exercises only the structural surface, so this is a known-acceptable gap. +- *Single-consumer dependency.* The fixture exists exclusively for `host_subprocess.rs`. If that test were retired, the fixture would become dead code; conversely, the test cannot be expanded to cover behaviours the fixture doesn't model without growing the fixture. Pre-existing carryover issue `clarion-adeff0916d` (fixture-binary self-build) tracks one known sharp edge here. +- *Build-ordering coupling.* The walking-skeleton CI job depends on `cargo build --workspace --bins` running before `cargo nextest run` so the binary is on disk when `host_subprocess.rs` looks for it. This is documented in `CLAUDE.md` and codified in `.github/workflows/ci.yml`'s `walking-skeleton` job, but is an implicit dependency that would break if a future contributor used `cargo nextest run --workspace` without the prior `cargo build`. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/section-python-plugin.md b/docs/arch-analysis-2026-05-18-1244/temp/section-python-plugin.md new file mode 100644 index 00000000..4e5b52b5 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/section-python-plugin.md @@ -0,0 +1,78 @@ +## Python language plugin (`plugins/python`) + +**Location:** `plugins/python/src/clarion_plugin_python/` + +**Responsibility:** Out-of-process language plugin that ingests a single Python source file at a time, extracts module/class/function entities plus `contains`/`calls`/`references` edges, and serves them to the Rust core over a Content-Length-framed JSON-RPC 2.0 channel on stdin/stdout (the L4 protocol). + +**Key Components:** + +- `__main__.py` (15 lines) — installs the stdout discipline guard, then delegates to `server.main()`; threads the server's exit code out to the host (`__main__.py:14`). +- `server.py` (285 lines) — L4 JSON-RPC dispatch loop. Implements the five protocol methods exactly as the Rust host's typed `protocol.rs` expects: `initialize`/`initialized`/`analyze_file`/`shutdown`/`exit` (`server.py:226-261`). Owns `ServerState` (initialized flag, shutdown flag, captured `project_root`, lazy `PyrightSession`) and the `read_frame`/`write_frame` Content-Length codec with an 8 MiB symmetric cap matching ADR-021 §2b (`server.py:48`, `71-126`). `handle_initialize` captures the host-supplied `project_root` and embeds the Wardline probe result in `capabilities.wardline` (`server.py:141-153`). `handle_analyze_file` reads the file off disk, lazily constructs the `PyrightSession`, and calls `extractor.extract_with_stats(...)` (`server.py:177-221`). +- `extractor.py` (744 lines, +98 on this branch for B.8) — AST → wire-shape extractor. `extract_with_stats` parses the source with `ast.parse`, prepends exactly one `module` entity (B.2 §3 Q1), then recursively walks via `_walk` to emit one `function` per `FunctionDef`/`AsyncFunctionDef` and one `class` per `ClassDef` (`extractor.py:261-344`, `_walk` at `589-668`). `parent_id` and one `contains` edge per non-module entity satisfy ADR-026 decision 2's dual encoding (`extractor.py:107-117`, `671-677`). `_ReferenceSiteCollector` is the separate `ast.NodeVisitor` pass for B.5* reference sites (`extractor.py:358-485`), then `extract_with_stats` hands the function IDs to `call_resolver.resolve_calls` and the reference sites to `reference_resolver.resolve_references` (`extractor.py:338-342`). Same-id collisions are handled at the emit boundary: `_has_overload_decorator` recognises `@overload` / `@typing.overload` / `@typing_extensions.overload` and skips emission *and* recursion entirely (`extractor.py:567-586`, `624`); any other duplicate (aliased overload imports, `@singledispatch.register def _():` runs) is dropped first-wins with a stderr line and a `duplicate_entities_dropped_total` bump (`extractor.py:629-637`). +- `pyright_session.py` (1251 lines) — long-running `pyright-langserver --stdio` LSP client. See sub-section below. +- `call_resolver.py` (64 lines) — `CallResolver` `Protocol` plus `CallsRawEdge` / `UnresolvedCallSite` / `Finding` TypedDicts; `NoOpCallResolver` is the test stand-in (`call_resolver.py:49-64`). `PyrightSession` is the production implementation. +- `reference_resolver.py` (69 lines) — symmetric: `ReferenceResolver` `Protocol`, `ReferenceSite` dataclass, `ReferencesRawEdge` TypedDict, `NoOpReferenceResolver` (`reference_resolver.py:54-69`). +- `entity_id.py` (75 lines) — Python side of the L2 byte-for-byte ADR-003+ADR-022 entity-ID assembler. Validates `plugin_id` / `kind` against the grammar `[a-z][a-z0-9_]*`, refuses the `:` separator inside any segment, raises typed `EmptySegmentError` / `GrammarViolationError` / `SegmentContainsColonError`. Cross-validated against `fixtures/entity_id.json` row-by-row (`entity_id.py:66-75`). +- `qualname.py` (46 lines) — ADR-018 L7 canonical qualname. Pure-AST reconstruction of CPython's runtime `__qualname__`: walks the parent chain in reverse, prepending `parent..` for function ancestors and `parent.` for class ancestors (`qualname.py:32-46`). Lock-in: this string must equal what Wardline produces for the same definition, otherwise the cross-product join breaks. +- `wardline_probe.py` (56 lines) — L8 fail-soft Wardline probe. `importlib.import_module("wardline.core.registry")` plus `importlib.import_module("wardline")`, then a `packaging.version` half-open range check against the manifest's `[integrations.wardline].min_version` / `max_version` (`wardline_probe.py:36-56`). Returns one of three dicts: `{"status": "absent"}`, `{"status": "enabled", "version": ...}`, `{"status": "version_out_of_range", "version": ...}`. **Invoked once per session at `initialize`** (`server.py:151`), never per-file. The `wardline.core.registry` import is the named Loom-doctrine asterisk from `docs/suite/loom.md` §5; Sprint 1 only proves the import + version-pin handshake — REGISTRY is not yet consumed. +- `stdout_guard.py` (62 lines) — replaces `sys.stdout` with a `_GuardedTextStdout` that raises `StdoutGuardError` on any write; captures the real `stdin.buffer` / `stdout.buffer` byte streams for the framing codec to use (`stdout_guard.py:57-62`). Single-shot, called by `__main__` before the dispatch loop starts. +- `__init__.py` (3 lines) — `__version__ = "0.1.4"`. + +**Sub-section: `pyright_session.py` (1251 lines, ~17% of total plugin LOC)** + +This file is the entire pyright integration surface. Internal structure: + +- *Public class `PyrightSession`* (`:117-758`) — implements both the `CallResolver` and `ReferenceResolver` Protocols. Constructed lazily once per `analyze_file` session by `server.handle_analyze_file` and held on `ServerState.pyright` for the lifetime of the connection (`server.py:193-194`, closed in `shutdown` handler at `server.py:246-248`). Public surface: `__init__`/`__enter__`/`__exit__`/`close`/`resolve_calls`/`resolve_references`/`kill_for_test`/`stderr_thread_alive`. Constructor knobs (`init_timeout_secs=30`, `call_timeout_secs=5`, `max_restarts_per_run=3`, `max_reference_sites_per_file=2000`) are exposed for tests (`pyright_session.py:118-145`). +- *Process lifecycle* — `_ensure_process` (`:505-516`) lazily spawns; `_start_process` (`:536-599`) does `subprocess.Popen([pyright-langserver, --stdio], cwd=project_root, env=..., stdin/stdout/stderr=PIPE)` and immediately calls `_initialize` with the LSP `initialize` request (`:601-616`). `_resolve_executable` (`:618-625`) walks: absolute-path → `sys.executable`'s sibling directory (i.e. the active venv) → `shutil.which`. A stderr-drain thread (`_start_stderr_drain` `:634-640`, `_drain_stderr` `:642-649`) keeps the 64 KiB `_stderr_tail` ring populated for diagnostics; the thread is daemonised. +- *Restart / poison handling* — `_record_restart_or_poison` (`:518-534`) increments `_restart_count` and emits a `CLA-PY-PYRIGHT-RESTART` finding; after 3 restarts the session goes `_disabled = True` and emits one `CLA-PY-PYRIGHT-POISON-FRAME`. Five fail-soft `CLA-PY-PYRIGHT-*` finding subcodes are defined at the top of the file (`:34-41`). +- *LSP transport* — `_request` (`:651-670`) writes Content-Length-framed JSON and busy-loops on `_read_message` skipping mismatched-id frames; `_notify` (`:672-674`) is the no-response variant; `_read_message` (`:693-714`) reads headers + body using `_read_line`/`_read_exact`/`_wait_readable` helpers (`:1218-1247`) that enforce a per-call deadline via `select.select` on the pipe fd. +- *Call resolution* (`resolve_calls` + `_resolve_with_pyright` `:181-380`) — opens the file via `textDocument/didOpen`, issues `textDocument/prepareCallHierarchy` per function entity, then `callHierarchy/outgoingCalls` per returned item. Edges are grouped by source byte range; multi-target ranges produce one `ambiguous` edge with the candidate list in `properties.candidates` (per ADR-028 confidence tiers, `:359-369`). Two AST-side enrichers — `_ambiguous_dict_dispatches` and `_dunder_call_dispatches` (`:1003-1145`) — fold dict-of-callables and `__call__`-on-instance patterns that pyright doesn't track natively into the same `grouped` map. Always followed by `textDocument/didClose` in `finally:` (`:380`). +- *Reference resolution* (`resolve_references` + `_resolve_references_with_pyright` `:228-453`) — hard cap of 2 000 sites per file (emits `CLA-PY-PY-REFERENCE-SITE-CAP` and returns early, `:238-250`); per-site `textDocument/references` queries with annotation-fallback retry (`:411-422`); deduplicates by `(from_id, to_id)` accumulator and finalises with `_reference_accumulator_to_edge` (`:922-937`). All exceptions are caught at the boundary and converted to fail-soft results. +- *AST function-indexing helpers* (`_build_function_index`, `_collect_entities`, `_CallSiteVisitor`, `_DictDispatchVisitor`, `_DunderCallDispatchVisitor` `:760-1145`) — a parallel AST pass independent from `extractor.py`'s walker; necessary because `PyrightSession` needs LSP positions (line/character) for every function and class plus the per-function call-site index, neither of which the wire shape carries. + +**Dependencies:** + +- Inbound: Rust core's plugin host (`crates/clarion-core/src/plugin/host.rs`) spawns this plugin via the `clarion-plugin-python` console script; the host's typed `protocol.rs` (`InitializeResult`, `AnalyzeFileResult`, `AnalyzeFileStats`, `ShutdownResult`) is the wire contract; the host's writer-actor (`clarion-storage`) consumes the emitted entities and edges; the `walking-skeleton` CI job invokes the full pipeline. +- Outbound: `pyright==1.1.409` (LSP server subprocess, pinned in both `pyproject.toml:20` and `plugin.toml:29`); `packaging>=24` (version-range parsing in the Wardline probe); Python stdlib only otherwise (`ast`, `json`, `subprocess`, `select`, `threading`, `importlib`, `pathlib`, `urllib.parse`). `wardline` is a **soft** outbound dependency — imported only to probe at `initialize`; absence is not an error. The doctrine asterisk noted in `docs/suite/loom.md` §5 is real: `wardline.core.registry` is imported by name (`wardline_probe.py:38`), and the manifest pins `[integrations.wardline] min_version=1.0.0 max_version=2.0.0` (`plugin.toml:48-55`). + +**Patterns Observed:** + +- **Protocol-typed wire boundary.** Every method handler returns a TypedDict whose shape mirrors the Rust host's serde structs exactly (`server.py:7-19` docstring enumerates this). The five JSON-RPC error codes used (`-32600`, `-32601`, `-32603`, `-32002`) are LSP-style (`server.py:51-54`). Out-of-spec frames raise `ProtocolError`, which propagates out of the loop and exits with status 1 (`server.py:284-285`). +- **Fail-soft pyright integration.** Every external failure mode of `pyright-langserver` (not installed, install-check rejection, init timeout, runtime timeout, transport-closed, broken pipe, OSError) is caught at the `resolve_calls` / `resolve_references` boundary, downgraded to a `CLA-PY-PYRIGHT-*` finding, and returned as "unresolved" counts in the result — never raised back into the dispatch loop (`pyright_session.py:202-217`, `265-280`). The 3-restart cap then disables the session entirely for the run. +- **Two-pass AST.** The extractor pass (`extractor.py`) produces wire entities + structural `contains` edges; a parallel AST pass inside `pyright_session.py` (`_build_function_index`, `_CallSiteVisitor`) builds the position-indexed function index pyright needs. The two never share a tree; this duplicates `ast.parse` work but keeps the extractor a pure function of source bytes. +- **`Protocol`-typed resolvers with No-Op fallback.** `CallResolver` and `ReferenceResolver` are `typing.Protocol`s with `NoOpCallResolver` / `NoOpReferenceResolver` defaults baked into `extractor.extract`'s kwargs (`extractor.py:83-84`, `247-249`). Tests can construct the extractor without spawning pyright. +- **Stdout-strictness via guard object.** `_GuardedTextStdout` raises rather than silently swallows; any library print() becomes a `StdoutGuardError`, which the dispatch boundary turns into a `_ERR_INTERNAL` JSON-RPC response (`server.py:259-260`). This is the plugin-side closure of WP2 UQ-WP2-08. +- **Path-jail-aware path handling.** `_resolve_module_path` relativises only the path used for the dotted qualname prefix; the wire `source.file_path` stays exactly as the host sent it, so the host's path-jail (which canonicalises against `project_root`) sees the original (`server.py:156-174`, `extractor.py:24-32`). +- **Single source of truth on ontology version.** The manifest declares `ontology_version = "0.5.0"` (`plugin.toml:46`); `server.py:36` redeclares the same constant `ONTOLOGY_VERSION = "0.5.0"`. Two declarations, no shared import — kept matched by hand per ADR-027. +- **B.8 fix layered defence.** The `@overload`-stub skip in `_has_overload_decorator` is the *fast path* for the named PEP 484 case; the same-id dedup loop in `_walk` is the *belt-and-suspenders* for anything the pattern-based check misses (aliased imports, `@singledispatch.register def _():`). Both feed the same wire-correctness invariant (no two entities with identical IDs) so the host's `UNIQUE(entities.id)` never trips mid-run (`extractor.py:283-294`, `624-637`, `645-652`). + +**Concerns:** + +- **Doctrine asterisk still live.** `wardline_probe.py:38` imports `wardline.core.registry` by name — exactly the Loom-doctrine asterisk called out in `docs/suite/loom.md` §5. Retirement condition is documented but not yet met. Not a defect; flagged because any architecture-quality review should know this is deliberate. +- **`ONTOLOGY_VERSION` is duplicated in two files (`server.py:36` and `plugin.toml:46`)** with no compile-time/runtime cross-check that they match. If a future ADR-027 minor bump updates one and forgets the other, the handshake validates the manifest value while the plugin behaves per the constant — silent skew. The comment at `server.py:38-41` acknowledges this and defers the manifest-flow-through. +- **`PyrightSession.close()` masks errors from the LSP `shutdown`/`exit` exchange** (`pyright_session.py:170`): timeouts, transport-closed, broken pipe, and `OSError` are all swallowed before the kill-and-wait. This is the correct behaviour at process-end, but it means a pyright that hangs on shutdown gives no signal beyond the eventual `process.kill()`. +- **`_resolve_with_pyright` busy-loops on mismatched `id` responses** (`pyright_session.py:663-666`). If pyright ever sends a stream of id-mismatched frames between request and response (server-initiated notifications, mismatched-cancel ack), the loop just keeps reading until the per-call deadline fires. The deadline upper-bounds it (5 s default), so this is bounded rather than fatal. +- **`_resolve_module_path`'s fall-through to the raw path on `ValueError`** (`server.py:170-173`) writes the absolute path into `source.file_path` of every emitted entity, which the host's path-jail check will reject. The comment says this is intentional ("fall back to the raw path so the host's logs show the drift"); whether that's the right failure mode versus an explicit per-file error finding is a design call worth noting for axiom-system-architect. +- **AST re-parse duplication.** `extractor.py` and `pyright_session._build_function_index` each call `ast.parse` on the same source bytes for every `analyze_file`. At elspeth-scale (~425k LOC Python) this is two AST walks per file, not one. Not yet measured; called out because the B.8 scale test on this branch is exactly where this would surface. + +**Confidence:** High — Read in full: `plugin.toml`, `pyproject.toml`, `server.py` (285), `extractor.py` (744), `qualname.py` (46), `wardline_probe.py` (56), `entity_id.py` (75), `stdout_guard.py` (62), `call_resolver.py` (64), `reference_resolver.py` (69), `__init__.py`, `__main__.py`. Sampled `pyright_session.py` top-level structure (every `def`/`class` declaration line) plus full reads of `__init__`, `close`, `resolve_calls`, `resolve_references`, `_resolve_with_pyright`, `_ensure_process`, `_record_restart_or_poison`, `_start_process`, `_initialize`, `_resolve_executable`, `_subprocess_env`, `_start_stderr_drain`, `_drain_stderr`, `_request`, `_notify`, `_live_process`, `_write_message`, `_read_message`. Cross-validated: B.8 `@overload` commit `29f0426` body cited verbatim, manifest pyright pin matches `pyproject.toml` pin (`1.1.409` in both `plugin.toml:29` and `pyproject.toml:20`), Wardline probe is initialize-only (single call site at `server.py:151`), the doctrine asterisk import path matches `loom.md` §5's wording. Tests directory inventory matches source-file inventory 1:1 (10 source files, 10 test files including `test_round_trip.py`). + +**Information Gaps:** + +- Did not exhaustively read `pyright_session.py` lines 715-1247 (the AST function-indexing helpers, dict-dispatch visitor, byte/position translators). Sampled enough to confirm shape but not every branch. +- Did not read the test files (`tests/test_*.py`); test coverage claims would require that step. +- Did not verify wire-shape claims by running the e2e script (`tests/e2e/sprint_1_walking_skeleton.sh`); compatibility is asserted from the Python TypedDicts vs. the Rust `protocol.rs` docstring at `server.py:7-19`, not from a live run on this branch. +- Did not chase `clarion-core/src/plugin/host.rs:132-154` to confirm the `RawEntity` / `RawSource` shape claim cited in `extractor.py:8-22`. Treated as authoritative because the extractor docstring is dated to the same commit family as the host. + +**Caveats:** + +- LOC counts via `wc -l` include blank lines and docstring lines. The "actual code" share is lower; `extractor.py:1-54` is all docstring, for instance. +- "B.8 +98 lines on this branch" is taken from the discovery-findings document's framing; I did not run `git diff main...HEAD -- extractor.py | wc -l` to verify exactness, but the commit `29f0426` body matches the behaviour read in `extractor.py:567-668`. +- The `wardline_probe` integration is described as "fail-soft" based on the three return shapes; whether downstream consult-mode briefings actually do anything different when `status == "enabled"` versus `"absent"` is out of scope for this entry (it would require reading the MCP briefing assembler). + +**Risk Assessment:** + +- *Doctrine asterisk surface.* The `wardline.core.registry` import (`wardline_probe.py:38`) is a known, ratified asterisk under `loom.md` §5 — risk is bounded by the documented retirement condition, but it remains a point where the federation axiom is consciously bent. Any review must surface it. +- *Wire-shape skew risk.* The plugin re-declares `ONTOLOGY_VERSION = "0.5.0"` (`server.py:36`) and `entity_kinds`/`edge_kinds`/`rule_id_prefix` (`plugin.toml:35-39`) as parallel sources of truth with the host's `protocol.rs`. Skew here would surface only at the handshake — the host's validator rejects mismatched `ontology_version` per ADR-027, so the risk is detected, not silent. +- *Pyright-availability dependency.* The walking-skeleton CI job and any `analyze` run that requests `calls` or `references` edges hard-depends on `pyright-langserver` resolvable via PATH, the active venv, or absolute path (`pyright_session.py:618-625`). On hosts without Node, the plugin still ships entities (the no-op fallback path), but every function emits as "unresolved" — observable but not catastrophic. +- *B.8 scale-test risk.* This branch (`sprint-2/b8-scale-test`) is precisely the change that hardens the extractor against the failure mode it was discovered under (UNIQUE collision on `@overload` stubs at elspeth scale). The fix is layered (semantic skip + safety-net dedup); the residual risk is aliased-overload imports plus identical-qualname intentional redefinitions, both of which now hit the safety-net path and log to stderr rather than crash. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/validation-02-subsystem-catalog.md b/docs/arch-analysis-2026-05-18-1244/temp/validation-02-subsystem-catalog.md new file mode 100644 index 00000000..0ff48a3f --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/validation-02-subsystem-catalog.md @@ -0,0 +1,71 @@ +# Validation report — 02-subsystem-catalog.md + +## Status +NEEDS_REVISION (warnings) + +## Summary +The catalog substantially meets the contract: all six subsystems are present with the required sections (Location, Responsibility, Key components, Inbound/Outbound dependencies, Patterns, Concerns, Confidence); every entry cites file:line and assigns an explicit, reasoned confidence; cross-cutting concerns from discovery §5 are reflected. One **internal factual contradiction** survived the assembly: the `clarion-core` entry states `clarion-plugin-fixture` does not depend on `clarion-core`, while the index table, the fixture entry, and the actual `Cargo.toml` agree it does. The error is a single sentence and does not propagate elsewhere, so it is a documentation defect, not a structural one. Several minor LOC drifts (e.g. `clarion-mcp/src/lib.rs` documented as 2620, actually 2623) should be reconciled in a sweep but do not invalidate analysis. + +## Findings + +### Critical (block proceed) +- None. + +### Warnings (document as tech debt, ok to proceed) + +1. **Factual contradiction inside the `clarion-core` entry — fixture dependency.** + Catalog line 123 (in the `clarion-core` Inbound block) says: + > *"`clarion-plugin-fixture` does **not** depend on `clarion-core` — the fixture binary speaks the wire protocol directly without sharing types."* + This is false. `crates/clarion-plugin-fixture/Cargo.toml:18` declares `clarion-core = { path = "../clarion-core", version = "0.1.0-dev" }`, and `crates/clarion-plugin-fixture/src/main.rs` opens with three `use clarion_core::plugin::...` lines pulling in `ContentLengthCeiling`, `Frame`, `read_frame`, `write_frame`, plus seven protocol envelope types. The Subsystem Index row E (catalog line 17) correctly shows outbound `core (types only)`, and the fixture entry (catalog lines 524, 536–540) correctly describes the dependency as "Protocol-by-shared-types" via `clarion-core`. The contradiction is local to the one parenthetical in the `clarion-core` entry. Fix: delete or invert the sentence at catalog line 123 to read "`clarion-plugin-fixture` depends on `clarion-core` for the typed protocol structs only (dev-dependency surface); it does not link against the supervisor / writer / MCP paths." This was the contradiction explicitly flagged by the task brief. + +2. **LOC drift between discovery, catalog, and on-disk files.** + - `clarion-mcp/src/lib.rs`: discovery says 2617, catalog says 2620, file is 2623. Acceptable drift (the file grew during B.8) but the catalog cites specific line ranges (e.g. "lines 296–319 for `tool_entity_at`") that will skew slightly. Recommend the line-range table be re-checked against the post-B.8 file or a commit SHA pinned to the analysis date. + - `clarion-core/src/plugin/host.rs`: catalog and discovery both 3126, file is 3126. Clean. + +3. **Catalog claims `clarion-mcp` issues exactly one raw SQL query bypassing `clarion-storage` (`reference_neighbors`).** Verified true (`crates/clarion-mcp/src/lib.rs:2381` is the sole `conn.prepare(` site). The catalog's "Concerns" line on schema coupling stands without modification. + +4. **The "Subsystem index" header row shows production LOC totals but does not call out that "Inbound deps" for the index excludes dev-dependencies.** The `clarion-cli` row reads inbound = `(binary — none)`, but `clarion-cli/Cargo.toml:[dev-dependencies]` lists `clarion-plugin-fixture`. This is a strict reading of "Rust library inbound" and is internally consistent with the rest of the catalog, but a future reader skimming the table may infer that the fixture is never linked by CLI. Recommend a footnote under the index table clarifying scope. + +5. **No "Confidence" header convention drift.** The contract calls for an explicit Confidence section; all six entries provide one (variously called "Confidence" or "Confidence Assessment"). No revision required; flagging for consistency. + +### Spot-checks performed + +| # | Claim | Verification | Result | +|---|---|---|---| +| 1 | `clarion-core/src/plugin/host.rs` is 3126 LOC, production code ~1450 LOC | `wc -l` = 3126; `grep '^#\[cfg(test)\]'` returns line 1451; production = lines 1–1450 | ✓ matches catalog | +| 2 | `clarion-mcp/src/lib.rs` is 2620 LOC | `wc -l` = 2623 | Drift +3 (B.8 follow-up commits); not material | +| 3 | `clarion-storage` has 9 `WriterCmd` variants | grepped `commands.rs`: `BeginRun`, `InsertEntity`, `InsertEdge`, `InsertInferredEdges`, `UpsertSummaryCache`, `TouchSummaryCache`, `ReplaceUnresolvedCallSitesForCaller`, `CommitRun`, `FailRun` | ✓ exactly 9 | +| 4 | Migration is 289 LOC with ADR-031 CHECKs on `edges.confidence`, `findings.{kind, severity, status}`, `runs.status` | `wc -l` = 289; CHECK clauses at lines 90 (`edges.confidence`), 108 (`findings.kind`), 112 (`findings.severity`), 125 (`findings.status`), 153 (`summary_cache.stale_semantic`), 201 (`runs.status`) | ✓ matches; catalog also correctly notes `stale_semantic` (line 236 of catalog) which is the additional one | +| 5 | `clarion-mcp` has exactly one raw SQL query (`reference_neighbors`) | Only `conn.prepare(` site in the crate is `lib.rs:2381`, inside `fn reference_neighbors` at `lib.rs:2366` | ✓ exactly one; matches catalog claim | +| 6 | Python plugin's `wardline_probe.py` imports `wardline.core.registry` by name | `wardline_probe.py:38: importlib.import_module("wardline.core.registry")`; `loom.md:70` names this exact asterisk | ✓ verbatim match | +| 7 | `clarion-plugin-fixture` depends on `clarion-core` (resolving the catalog's internal contradiction) | `Cargo.toml:18` and three `use clarion_core::plugin::*` lines in `main.rs` | ✓ depends on it; **catalog `clarion-core` entry is wrong**; fixture entry and index row are correct | +| 8 | `llm_provider.rs` is 948 LOC; OpenRouter strict-JSON path lives at `response_format_for_purpose` with `"strict": true` for both purposes | `wc -l` = 948; `response_format_for_purpose` at line 297; `"strict": true` at lines 303 and 333 | ✓ matches catalog | +| 9 | `pyright_session.py` is 1251 LOC | `wc -l` = 1251 | ✓ matches | +| 10 | `extractor.py` is 744 LOC; `@overload`-stub skip via `_has_overload_decorator` plus safety-net dedup | `wc -l` = 744; `_has_overload_decorator` at line 567; first-wins dedup via `state.duplicate_entities_dropped` at lines 630, 647 | ✓ matches | + +### Cross-document consistency +- **Bidirectionality of dependency claims.** Spot-checked four directional claims; all consistent. + - `clarion-storage` outbound to `clarion-core` (`EdgeConfidence` only) ↔ `clarion-core` is *not* listed as a consumer of `clarion-storage` anywhere ↔ `Cargo.toml` shows `clarion-storage` deps on `clarion-core` but not vice-versa. ✓ + - `clarion-mcp` outbound to both `clarion-core` and `clarion-storage` ↔ both entries acknowledge inbound from `clarion-mcp`. ✓ + - `clarion-cli` outbound to all three core/storage/mcp ↔ each of those entries lists `clarion-cli` as inbound. ✓ + - Python plugin "subprocess of host" ↔ `clarion-core` entry's `host.rs::spawn` description matches; no Rust-link relationship, only stdio + on-disk discovery. ✓ +- **Coverage of cross-cutting concerns from discovery §5.** All seven items (entity-ID format, JSON-RPC L4, ontology version semver, edge confidence tiers, summary-cache 5-tuple, Loom federation doctrine, ADR-031 schema-validation policy) appear in catalog entries: + - Entity-ID format: in `clarion-core` (entity_id.rs, 610 LOC, ADR-003 parity). + - JSON-RPC L4: in `clarion-core/protocol.rs`, fixture entry "Protocol-by-shared-types", Python plugin `server.py`. + - Ontology version: in `clarion-storage` schema discussion and Python plugin's `ONTOLOGY_VERSION` duplication concern. + - Edge confidence tiers: in `clarion-storage::enforce_edge_contract` and `clarion-mcp::optional_confidence`. + - 5-tuple cache key: in `clarion-storage::cache` and `clarion-mcp::read_summary_inputs`. + - Loom doctrine: in Python plugin entry's "Doctrine asterisk still live" concern, and `clarion-mcp::filigree` enrich-only discussion. + - ADR-031: in `clarion-storage` (CHECK constraints discussion and edge contract). +- **Sprint-2 deltas from discovery §7.** All represented: + - new `clarion-mcp` crate — full entry C exists. + - OpenRouter strict-JSON path — `clarion-core/llm_provider.rs` entry discusses it at lines 92–94 and 150 of catalog. + - ADR-031 CHECK clauses — `clarion-storage` entry, lines 236+. + - B.8 `@overload`-stub fix — Python plugin entry, lines 579 and 614–615. + +### Notes +- The catalog is well-evidenced: ~80+ file:line citations spot-check as accurate. +- "Confidence" sections in five of six entries explicitly state what was read in full vs sampled (e.g., `clarion-mcp` entry: "Read 100% of `config.rs`…sampled five handler bodies in full…"). This level of detail is unusually high for the contract and is a strength. +- The Python plugin entry's "AST re-parse duplication" concern is a genuinely novel observation surfaced by the per-subsystem pass, not echoed in discovery; flagging as a value-add. +- The dead-stub finding in `clarion-mcp` ("Dead stateless `handle_tool_call` stub", catalog line 373) is also a fresh observation; verified at `lib.rs:1701` as a real footgun. +- Suggested edit ordering (low cost): (a) fix the fixture/clarion-core sentence at catalog line 123; (b) update mcp lib.rs LOC to 2623 or pin a commit SHA at the head of the catalog; (c) add a footnote under the Subsystem Index that "Inbound deps" excludes `[dev-dependencies]`. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/validation-03-diagrams.md b/docs/arch-analysis-2026-05-18-1244/temp/validation-03-diagrams.md new file mode 100644 index 00000000..d6af2043 --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/validation-03-diagrams.md @@ -0,0 +1,97 @@ +# Validation Report — 03-diagrams.md + +**Document:** `/home/john/clarion/docs/arch-analysis-2026-05-18-1244/03-diagrams.md` +**Validator:** analysis-validator (independent pass) +**Date:** 2026-05-18 +**Status:** APPROVED + +--- + +## Summary + +Five C4-inspired diagrams (Context, Container, two sequences, one component zoom). All Mermaid blocks parse cleanly; captions accurately describe what each diagram shows. Spot-checks against the catalog and source code confirm every substantive claim. All six subsystems from the catalog appear in at least one diagram. Loom-doctrine relationships (Filigree enrich-only, Wardline soft-import asterisk) are represented in the L1 view. ADR-007 5-tuple cache, edge-contract validator, writer-actor, and the host validator pipeline each have visible representation. + +No critical issues. Two minor notes recorded as informational; neither blocks progression. + +--- + +## Findings + +### Critical + +None. + +### Warnings + +None. + +### Spot-checks (all PASS) + +1. **Storage → Core dependency labelling (Diagram 2).** + The user's framing of the question pointed at `STORAGE → CORE` labelled "writer + readers". Re-reading the Mermaid source: the `"writer + readers"` label is actually on `STORAGE -->|"writer + readers"| DB` (line 99), not on `STORAGE --> CORE` (line 93). The latter is unlabelled, which is correct shorthand — the catalog records the dep as `EdgeConfidence` only (`crates/clarion-storage/src/query.rs:6`, `commands.rs:14`), and the diagram's prose at line 105 explicitly states "`storage` → `core` (one symbol, `EdgeConfidence`)". **PASS — no misleading label exists.** + +2. **`SoftFailed` "partial work kept" (Diagram 3).** + Verified at `crates/clarion-cli/src/analyze.rs:478–509`. The `SoftFailed` branch sends `WriterCmd::CommitRun { status: RunStatus::Failed, stats_json, … }` where `stats_json` includes `entities_inserted`, `edges_inserted`, etc. The writer-actor folds the `UPDATE runs SET status='failed'` into the open entity transaction (per the comment at line 479–482 and the catalog's storage section), so accepted entities from healthy plugins persist alongside the failure marker. The diagram's "partial work kept" caption is accurate. **PASS.** + +3. **ADR-007 5-tuple cache key (Diagram 4).** + Verified at `crates/clarion-mcp/src/lib.rs:1077–1083`. `SummaryCacheKey` is materialised with exactly the five fields shown: `(entity_id, content_hash, prompt_template_id, model_tier, guidance_fingerprint)`. `prompt_template_id` is set to `LEAF_SUMMARY_PROMPT_TEMPLATE_ID`, defined at `crates/clarion-core/src/llm_provider.rs:10` as `"leaf-v1"`. The diagram's annotation `LEAF_SUMMARY_PROMPT_TEMPLATE_ID = "leaf-v1"` matches. (The context-line citation `1010-1016` in the user's request actually points at `InferredEdgeCacheEntry`, not `SummaryCacheKey` — the diagram itself doesn't cite line numbers and shows the correct 5-tuple, so this is irrelevant to the diagram's correctness.) **PASS.** + +4. **Five validator steps, kill paths on 3 and 4 only (Diagram 5).** + Verified at `crates/clarion-core/src/plugin/host.rs:1031–1198`. + - Step 0 field-size (lines 1103–1107): `continue` only — drops record. + - Step 1 ontology declared-kind (1110–1114): `continue` only. + - Step 2 identity (1117–1133): `continue` only. + - Step 3 jail (1135–1164): `continue` on under-threshold escape; `return Err(HostError::PathEscapeBreakerTripped)` at line 1160 after `do_shutdown` — **kill path confirmed**. + - Step 4 entity cap (1166–1179): `return Err(HostError::EntityCapExceeded(e))` at line 1178 after `do_shutdown` — **kill path confirmed**. + Steps 0–2 have no `return Err` path; only `continue`. The diagram's claim "steps 3 and 4 are the only ones with kill paths" is exact. **PASS.** + +5. **60-second in-flight coalescer timeout (Diagram 4 caption).** + Verified at `crates/clarion-mcp/src/lib.rs:912` — `tokio::time::timeout(std::time::Duration::from_secs(60), rx.recv())` inside `coalesced_inferred_dispatch` (declared at line 894). The `inferred_inflight: HashMap>` field is at lines 175–176. **PASS.** + +### Coverage check (PASS) + +| Catalog subsystem | Appears in | +|---|---| +| A `clarion-core` | Diagrams 2 (CORE), 3 (CORE), 5 (entire diagram) | +| B `clarion-storage` | Diagrams 2 (STORAGE), 3 (WRITER + DB), 4 (READER, CACHE, WRITER) | +| C `clarion-mcp` | Diagrams 2 (MCP), 4 (MCP) | +| D `clarion-cli` | Diagrams 2 (CLI), 3 (CLI) | +| E `clarion-plugin-fixture` | Diagram 2 (FIXTURE), Diagram 3 (as alternative to PLUGIN) | +| F Python plugin | Diagrams 1 (PYRIGHT external + implicit), 2 (PYPLUGIN), 3 (PLUGIN) | + +Loom doctrine surfaces (Diagram 1): Filigree as solid `sibling`-styled box with "enrich-only" edge label; Wardline as solid sibling with a dashed "import probe at handshake (asterisk: loom.md §5)" edge — matches `docs/suite/loom.md` §5's named v0.1 asterisk treatment. + +Architecturally load-bearing concepts (all visible): +- **ADR-007 5-tuple cache** — Diagram 4, explicit 5-tuple shown in `SELECT by 5-tuple` step. +- **Edge-contract validator** — Diagram 3, `InsertEdge * N (enforce_edge_contract)` step. +- **Writer-actor (ADR-011)** — Diagrams 2, 3, 4 (singleton WRITER participant in both sequences). +- **Host validator pipeline** — Diagram 5 (entire diagram). + +### Notes (informational, non-blocking) + +1. **Diagram 3 plugin-loop step ordering is slightly idealised.** The diagram shows the `loop per file in plugin extensions` nested inside `loop per plugin`, with `host.shutdown / kill / reap` happening after the inner loop completes. In `clarion-cli/src/analyze.rs` the actual control flow uses a `BatchResult`-returning helper and per-plugin spawn-then-collect pattern; the diagram's nesting reads as a clean conceptual model rather than a literal call-graph. The diagram's caption doesn't claim line-fidelity, so this is acceptable shorthand for an L3 sequence. + +2. **Diagram 5 collapses edge/stats post-processing into terminal nodes.** Steps `EDGES` (process_edges, drop-only) and `STATS` (process_stats) are shown as siblings of the entity validator chain, attached to `OUTCOME` rather than to the accepted-entity exit. The host actually invokes `process_edges` and `process_stats` after the per-entity loop completes (`host.rs:1190–1191`). The diagram's edge layout is a fair simplification; the design-notes prose underneath ("same drop-on-violation discipline is applied to edges, but with no kill paths") sets expectations correctly. + +--- + +## Confidence Assessment + +**High.** All five substantive spot-checks resolved cleanly against source code at the cited locations. Coverage is complete. The diagrams are unusually well-aligned with the catalog and source — captions are accurate, none of the labels overstate what's shown, and the L1/L2/L3 + sequence breakdown is conventionally correct C4 usage. + +## Risk Assessment + +**Low.** No claims that would mislead a downstream consumer. The minor "notes" above are stylistic — the diagrams are read as conceptual models, not literal call traces, and their captions are consistent with that contract. + +## Information Gaps + +None blocking. The diagrams deliberately omit a `clarion-mcp::lib.rs` component view and a writer-`WriterCmd` zoom; both omissions are explicitly justified in the "Coverage notes" table at the end of the document and adequately substituted by catalog content. + +## Caveats + +- This validation checks structural and factual fidelity against the catalog and source spot-checks; it does not re-render the Mermaid blocks. The document attests the blocks were validated through the Mermaid renderer during authoring. +- Architectural quality of the chosen abstractions (e.g. is a "Container" view the right level for `clarion-mcp`?) is out of scope for structural validation. Refer to `axiom-system-architect:architecture-critic` if such review is desired. + +--- + +**Final status: APPROVED** — proceed to next phase. diff --git a/docs/arch-analysis-2026-05-18-1244/temp/validation-04-final-report.md b/docs/arch-analysis-2026-05-18-1244/temp/validation-04-final-report.md new file mode 100644 index 00000000..a14ef2ec --- /dev/null +++ b/docs/arch-analysis-2026-05-18-1244/temp/validation-04-final-report.md @@ -0,0 +1,116 @@ +# Validation — `04-final-report.md` + +**Validator:** axiom-system-archaeologist:analysis-validator +**Date:** 2026-05-18 +**Target:** `docs/arch-analysis-2026-05-18-1244/04-final-report.md` +**Status:** **NEEDS_REVISION (warnings)** — structurally complete, all required sections present, internally consistent on priority mapping; multiple stale numeric facts at the §1 / §5 / §6 level that drifted between the catalog pass and the report write-up. None of the drifts invalidate the report's architectural conclusions, but the report explicitly bills itself as evidence-anchored, and the numbers cited in the executive summary and the deltas section must match the working tree. + +--- + +## Summary + +The report covers every contract-required section (executive summary; architecture at a glance; per-subsystem walkthrough for all 6 subsystems; cross-cutting concerns table; prioritised observations & risks; Sprint-2 deltas; recommended follow-ups; confidence + limitations + audit trail). Risk priorities in §5 and recommendation priorities in §7 are mapped one-to-one (3 High → items 1–3; 5 Medium → items 4–8; 8 Low → items 9–16). The §8 audit-trail file list matches the actual workspace contents (1 coordination + 1 discovery + 1 catalog + 1 diagrams + 1 report + 6 section-*.md + 2 validation-*.md). Cross-cutting concerns enumerate 14 entries grounded in ADR or doctrine citations. + +The report is fit for an architect handover at the level of structure, narrative, and prioritisation. The blocker is a cluster of stale numbers that the report inherited from the catalog pass and that drifted further before the report was written. + +--- + +## Findings + +### Critical + +None. No claim is contradicted by primary evidence in a way that changes a conclusion. The drifts below are warnings, not blockers. + +### Warnings + +**W-1. `lib.rs` LOC stale by ~90 lines.** +Report §1 ("Standout strengths") and §2 ("Read surface") cite `clarion-mcp/src/lib.rs` at **2 623 LOC**. Working tree on `sprint-2/b8-scale-test` HEAD shows **2 712 LOC** (`wc -l crates/clarion-mcp/src/lib.rs`). The catalog footnoted the prior drift (2 620 → 2 623); two further commits on this branch (`7317a91` clippy-explicit Map; `87036b1` reservation-poison fix; `363bb0a` inferred-target pre-filter) appear to have pushed the file past 2 700 since the catalog pass. Recommend re-running `wc -l` against the working tree and updating §1, §2 table, §3.3, and §6 "drift from 2620 to 2623" parenthetical. + +**W-2. "11 commits ahead of `main`" is now 17.** +Report header line 4 and §6 paragraph "Current branch (`sprint-2/b8-scale-test`) vs. `main`". Verified by `git rev-list --count main..HEAD` → **17**. The discovery doc (01) also says 11 — the figure was correct at the start of the analysis and stale by the time the report was written; four additional commits landed on the branch between discovery and report-writing: `caa6459` (B.8 raw artifacts), `f7bb63f` (CLAUDE.md refresh), `7317a91` (clippy), `87036b1` (poison fix), `363bb0a` (pre-filter inferred). Two of those (`87036b1`, `363bb0a`) are substantive MCP source-code changes that should plausibly join the §6 list of "substantive source changes" if the report wants to remain accurate at the commit level. + +**W-3. `git diff --stat main..HEAD` numbers are stale.** +Report §6 reports "45 files changed, 23 209 insertions, 59 deletions". Verified `git diff --stat main..HEAD | tail -1` → **59 files changed, 25 650 insertions, 85 deletions**. Same root cause as W-2 — the same five commits landed after the figures were captured. + +**W-4. Spot-check M-1 line-number is wrong.** +Report §5 M-1 cites `clarion-mcp/src/lib.rs:2381` as the location of `reference_neighbors`'s `conn.prepare(`. Verified: the only `conn.prepare(` site in the crate is at **line 2470**; the `reference_neighbors` fn itself begins at **line 2455**. The *claim* M-1 makes ("the only `conn.prepare(` site in the crate") is correct — only the line number is stale. The catalog also stated `reference_neighbors` is at "lib.rs:2363–2400" / "line 2378", which is also stale by the same +80 lines as W-1. Recommend either re-running grep at report-emit time or footnoting the line-number-as-of-commit. The Concern-level claim survives. + +**W-5. Sprint-2 deltas listing presented as 7 items but worth bullet count check.** +Report §6 paragraph "Whole-of-Sprint-2" lists six bullets B.2–B.8 plus "OpenRouter swap" — actually seven bullets. The narrative claim above the bullets ("Six merged work-package landings since `v0.1-sprint-1`") undercounts by one. Either the narrative count is wrong (should be seven) or "OpenRouter swap" is being mentally excluded (in which case the list should say so explicitly). Trivial to fix. + +### Spot-check results + +| # | Claim | Source line | Result | +|---|---|---|---| +| 1 | §5 H-1: `analyze.rs:478–509` is the `SoftFailed` branch that folds `UPDATE runs SET status='failed'` into the open entity transaction | `crates/clarion-cli/src/analyze.rs:478–509` | **CONFIRMED** — `RunOutcome::SoftFailed { reason }` arm at 478, `CommitRun { status: RunStatus::Failed, ... }` at 499–501, `"CommitRun(Failed) — soft fail"` context at 508. | +| 2 | §5 M-1: `clarion-mcp/src/lib.rs:2381` is the only `conn.prepare(` site in the crate | `grep -n 'conn.prepare(' crates/clarion-mcp/src/lib.rs` | **PARTIAL** — exactly one `conn.prepare(` site (claim survives); line number is **2470**, not 2381 (W-4). | +| 3 | §4: ADR-031 added six CHECK clauses | `crates/clarion-storage/migrations/0001_initial_schema.sql` | **CONFIRMED** — `grep -cE 'CHECK\s*\(' ...sql` → **6**: `edges.confidence` (90), `findings.kind` (108), `findings.severity` (112), `findings.status` (125), `summary_cache.stale_semantic` (153), `runs.status` (201). | +| 4 | §1: no god-files. The two largest source files are coherent, banded, internally documented; `host.rs` ~3 126 LOC, `lib.rs` ~2 623 LOC | `wc -l crates/clarion-core/src/plugin/host.rs crates/clarion-mcp/src/lib.rs` | **PARTIAL** — `host.rs` 3 126 ✓; `lib.rs` actually **2 712** (W-1). The "no god-files" architectural judgment is unaffected. | +| 5 | §6: 11 commits ahead of main | `git rev-list --count main..HEAD` | **WRONG** — actually **17** (W-2). | +| 6 | §1: 24 462 Rust LOC across 5 crates; 5 629 Python; 78 markdown docs | `find` + `wc -l` | **PARTIAL** — Rust now **24 727** (drift +265, same root cause as W-1/W-2); Python 5 629 ✓; markdown actually **91** files in `docs/` tree (`find docs -name '*.md' \| wc -l`). The "78 markdown docs" figure in §1 also disagrees with discovery doc 01 §1.1 which says "79 .md files" — the two source documents already disagreed before the report was written. | + +### Notes (non-blocking) + +**N-1. §3.3 "Three source files" claim.** +"One Rust crate, three source files (`lib.rs` 2 623 + `config.rs` 352 + `filigree.rs` 238)" — correct count, stale LOC for `lib.rs` (W-1). Same drift, no extra issue. + +**N-2. §4 cross-cutting concerns: edge-ontology row labels three sites of duplication.** +"Hard-coded in `clarion-storage::writer.rs:394–401`; declared in `plugin.toml:38`; documented in ADR — **3-place duplication, no cross-check**." Catalog §clarion-storage §Concerns (per the report's own internal reference) backs this. Not validated against `writer.rs` line numbers in this pass — flagged as a candidate spot-check for any deeper validation. + +**N-3. §8 audit-trail listing omits dot-prefix grep-friendliness but otherwise matches.** +The listing labels `00-coordination.md` "coordination plan + execution log" — workspace `ls` confirms file exists. Sub-tree files (`temp/section-*.md`, `temp/validation-*.md`) all present. + +**N-4. §5.4 Doctrine-accepted risks (A-1 … A-4) are present and explicitly mark themselves "do not fix".** +This is the right framing for the federation asterisks and the file-size acceptances; matches discovery doc §5 and catalog §clarion-core §A-3. Worth keeping. + +**N-5. Information gaps section (§8) is candid and matches the actual scope of the pass.** +"Test coverage is not depth-read", "external siblings are not vendored", "B.8 result data not inspected" — all consistent with what the discovery and catalog passes actually did. Good limitation discipline. + +**N-6. Recommendations §7 ordering is risk-priority-first within tier and then by §5 letter.** +Item 1 = H-1, item 16 = L-8. Consistent. No "high" recommendation without a matching §5 High; no §5 High without a matching item. + +**N-7. Coverage check: every subsystem in the catalog has a §3 subsection in the report.** +A (`clarion-core`) → §3.1; B (`clarion-storage`) → §3.2; C (`clarion-mcp`) → §3.3; D (`clarion-cli`) → §3.4; E (`clarion-plugin-fixture`) → §3.5; F (`plugins/python`) → §3.6. No subsystem from the catalog is silently omitted. Every catalog "Concerns" entry (read at the heading level) is folded into §5 either as a numbered risk or as one of the doctrine-accepted A-* items. + +**N-8. No silent omission of cross-cutting concerns from discovery / catalog.** +The 14-row table in §4 covers entity-ID, JSON-RPC L4, plugin authority, ontology ownership, edge confidence, edge ontology, ontology semver, summary cache key, migration governance, schema-validation policy, federation axiom, Filigree bindings, summary scope, tooling baseline. Discovery §5 has 8 concerns — all 8 are in §4. Catalog cross-references are honoured. + +--- + +## Confidence Assessment + +- **Structural compliance:** High — every contract-required section is present in the correct order, properly cross-referenced to source artifacts. +- **Internal consistency:** High — risk-priority ↔ recommendation-priority mapping is one-to-one and complete. +- **Cross-document coverage:** High — every subsystem in the catalog has a walkthrough entry; every catalog concern entry maps to a §5 risk or §5.4 acceptance. +- **Numerical accuracy:** Medium — 5 of 6 spot-checks revealed stale figures inherited from the catalog or drifted further before report emit. The drifts are all "snapshot in motion" artefacts (LOC, commit count, diff stats) rather than misreadings of source. +- **Conclusion durability:** High — none of the stale numbers, if corrected, would change a §5 priority assignment or a §7 recommendation. + +## Risk Assessment + +- **Risk that downstream readers cite stale figures:** Medium. The report is explicitly the synthesis layer; a Sprint-3 plan citing "11 commits ahead", "lib.rs 2 623 LOC", or "45 files changed" will be wrong on day one of execution. +- **Risk that the file-size acceptance (A-4) shifts:** Low-Medium. The catalog argued `lib.rs` at 2 620 is coherent; at 2 712 the same argument still holds, but the file is on a measurable growth trajectory (+92 LOC across five commits on this branch alone). If §5.4 A-4 is to remain "do not fix", a "monitored, not accepted indefinitely" footnote would help. + +## Information Gaps + +- The report's "audit trail" §8 lists `temp/` contents in shape but does not record a hash or modification time. If the report is consumed weeks later, the validator artefacts may have drifted again. +- Several catalog line-number citations (e.g. `writer.rs:394–401` for `STRUCTURAL_EDGE_KINDS`, `lib.rs:1010–1016` for the 5-tuple cache key, `lib.rs:1180–1316` for `BudgetLedger.blocked`) were not independently re-verified in this validation pass — they may be subject to the same drift as W-1/W-4. +- The §6 narrative "Six merged work-package landings" / actually seven bullets discrepancy (W-5) suggests the deltas section was edited under time pressure. + +## Caveats + +- This is a structural-compliance validation, not a technical-accuracy validation. The architectural judgments in the report (e.g. "boundary discipline is real", "plugin separation is a process boundary not a trait abstraction", "no god-files") were not independently re-derived — they were checked for internal coherence with discovery and catalog, not against the source code as a quality assessment. A technical critique should go through `axiom-system-architect:assess-architecture` as the report itself notes. +- The line-number / LOC drift findings are inherently snapshot-bound; any document of this kind written against a live working tree carries the same risk. Recommend the analysis workspace pin a commit hash in each document's header so future readers can re-execute the spot-checks deterministically. + +--- + +## Recommendation + +**Status: NEEDS_REVISION (warnings).** Five low-effort edits unblock APPROVED: + +1. Re-run `wc -l crates/clarion-mcp/src/lib.rs` and update §1 (Standout strengths), §2 (Read surface table), §3.3 (first sentence), §6 ("from 2620 to 2623" parenthetical). +2. Re-run `git rev-list --count main..HEAD` and update the header line 4 and §6 first sentence of the "Current branch" paragraph. +3. Re-run `git diff --stat main..HEAD | tail -1` and update §6 "45 files changed, 23 209 insertions, 59 deletions". +4. Re-grep `conn.prepare(` and update the §5 M-1 line number (currently `:2381`, should be `:2470`). +5. Reconcile "Six merged work-package landings" with the seven bullets that follow — either say "Seven" or split the OpenRouter swap out of the merged-WP list explicitly. + +Pin a commit hash in the report header (e.g. `Commit: 363bb0a`) so future readers can re-derive every numeric claim deterministically. Then re-validate — expected pass. diff --git a/docs/clarion/adr/ADR-006-clustering-algorithm.md b/docs/clarion/adr/ADR-006-clustering-algorithm.md index a485e6c8..2e4230a0 100644 --- a/docs/clarion/adr/ADR-006-clustering-algorithm.md +++ b/docs/clarion/adr/ADR-006-clustering-algorithm.md @@ -1,13 +1,13 @@ -# ADR-006: Clustering Algorithm — Leiden on Imports+Calls Subgraph with Louvain Fallback +# ADR-006: Clustering Algorithm — Leiden on Imports+Calls Subgraph with Weighted-Components Fallback -**Status**: Accepted +**Status**: Accepted; amended by [ADR-032](./ADR-032-weighted-components-clustering-fallback.md) **Date**: 2026-04-18 **Deciders**: qacona@gmail.com **Context**: Phase 3 subsystem discovery takes module-level structural edges and produces `subsystem` entities; algorithm choice shapes downstream LLM cost and query quality ## Summary -Phase 3 clustering runs **Leiden** over a directed, weighted subgraph of module-level `imports` + `calls` edges, with edge weights equal to reference counts. The algorithm is seeded (for determinism), filters out clusters smaller than `min_cluster_size` (default 3), and records `modularity_score` on each resulting `subsystem` entity. **Louvain** is a configured fallback — selectable via `clarion.yaml:analysis.clustering.algorithm: louvain`. The fallback exists because Leiden implementations in Rust are less common than Louvain; if the vendored/chosen implementation proves unstable at implementation time, Louvain is the deterministic cutover. Both algorithms produce subsystem entities under the core-reserved `subsystem` kind (ADR-022), identified as `core:subsystem:{cluster_hash}` (ADR-003). No hard modularity pass/fail threshold ships in v0.1 — the score is reported, not enforced. +Phase 3 clustering runs **Leiden** over a directed, weighted subgraph of module-level `imports` + `calls` edges, with edge weights equal to reference counts. The algorithm is seeded (for determinism), filters out clusters smaller than `min_cluster_size` (default 3), and records `modularity_score` on each resulting `subsystem` entity. ADR-032 amends the original Louvain fallback into a deterministic **weighted-components** fallback, selectable via `clarion.yaml:analysis.clustering.algorithm: weighted_components` and used automatically only when Leiden emits zero or one community and the fallback emits more. Both algorithms produce subsystem entities under the core-reserved `subsystem` kind (ADR-022), identified as `core:subsystem:{cluster_hash}` (ADR-003). No hard modularity pass/fail threshold ships in v0.1 — the score is reported, not enforced. ## Context @@ -40,11 +40,11 @@ The trade-off: Leiden is less widely implemented than Louvain in the Rust ecosys - **Resolution parameter**: `γ = 1.0` default (standard modularity). Configurable via `clarion.yaml:analysis.clustering.resolution` if operators want finer or coarser communities. - **Iteration cap**: 100 passes (configurable). Most runs converge in <10. -### Fallback: Louvain +### Fallback: Weighted Components -- **Trigger**: `clarion.yaml:analysis.clustering.algorithm: louvain` explicit selection, *or* Leiden implementation-side failure detected at implementation time (this is an implementation-decision trigger, not a runtime fallback — if Leiden is broken at release, Louvain becomes the default for that release with an ADR revision). -- **Implementation**: `petgraph`-based; Louvain is simpler and the crate ecosystem offers stable options. -- **Behaviour delta**: Louvain may produce disconnected communities. Phase 3 post-processes Louvain output to split disconnected clusters by weakly-connected components, mitigating the defect at the cost of occasional fragmentation. +- **Trigger**: `clarion.yaml:analysis.clustering.algorithm: weighted_components` explicit selection, or runtime auto-fallback when `algorithm: leiden` returns zero or one community and weighted components returns more communities. +- **Implementation**: deterministic connected components over edges whose weight is at least the average positive edge weight. +- **Behaviour delta**: weighted components is an explainable local grouping fallback, not modularity optimisation. `properties.algorithm` and `runs.stats.clustering.algorithm` record the algorithm actually used. ### Output @@ -52,7 +52,7 @@ Each cluster above `min_cluster_size` (default 3) becomes a `subsystem` entity ( - `id`: `core:subsystem:{cluster_hash}` where `cluster_hash = sha256(sorted(member_module_ids))` truncated to 12 chars (ADR-003). - `properties`: - - `cluster_algorithm`: `"leiden"` or `"louvain"` + - `algorithm`: `"leiden"` or `"weighted_components"` - `modularity_score`: floating-point; reported, not enforced - `member_count`: integer - `synthesised_at`: timestamp (Phase-6 LLM-synthesised name/description; absent until Phase 6 runs) @@ -62,7 +62,7 @@ Each cluster above `min_cluster_size` (default 3) becomes a `subsystem` entity ( ### Quality assessment -No hard modularity threshold passes/fails in v0.1. Modularity scores below 0.3 are conventionally "weak" clustering; Phase 3 emits `CLA-FACT-CLUSTERING-WEAK-MODULARITY` (severity INFO) when the overall score falls below that. Operators see the signal but Phase 3 does not refuse to emit clusters. Block C1's cost-model spike will validate whether weak-modularity subsystems produce useful Opus output or wasted cost; a v0.2 decision may add a hard threshold with `--refuse-weak-modularity` semantics. +No hard modularity threshold passes/fails in v0.1. Modularity scores below `analysis.clustering.weak_modularity_threshold` (default `0.3`, set `0.0` to disable the finding) emit `CLA-FACT-CLUSTERING-WEAK-MODULARITY` (severity INFO). Operators see the signal but Phase 3 does not refuse to emit clusters. Block C1's cost-model spike will validate whether weak-modularity subsystems produce useful Opus output or wasted cost; a v0.2 decision may add a hard threshold with `--refuse-weak-modularity` semantics. ## Alternatives Considered @@ -74,7 +74,7 @@ Skip Leiden; use Louvain as the v0.1 algorithm. **Cons**: Louvain's disconnected-community defect is a semantic bug for subsystem membership. The post-processing split-by-connected-components mitigates but does not eliminate the problem — the resulting "subsystem A-1" and "subsystem A-2" are semantically two subsystems the algorithm failed to distinguish. Leiden produces the right answer in one step. -**Why rejected**: quality delta matters for Phase 6 Opus spend and query coherence; Leiden is the right answer and the implementation risk is absorbable via the Louvain fallback. +**Why rejected**: quality delta matters for Phase 6 Opus spend and query coherence; Leiden is the right answer and the implementation risk is absorbable via the weighted-components fallback. ### Alternative 2: Graph-neural community detection @@ -123,17 +123,17 @@ Operators declare subsystems in `clarion.yaml`; clustering is skipped. - Leiden's connected-community guarantee makes `CLA-FACT-TIER-SUBSYSTEM-MIXING` and subsystem-navigation MCP tools semantically sound — a "subsystem" is always a coherent group. - Phase 6's per-subsystem Opus call lands against meaningful clusters, not noise. Cost spend tracks semantically-relevant subsystems. - Determinism (seeded RNG) makes `--resume` and cross-run diffing of subsystem structure possible. Operators see "this module left subsystem X" as a real signal, not RNG noise. -- Louvain fallback absorbs implementation risk without redesigning the decision. +- Weighted-components fallback absorbs implementation risk without redesigning the decision. ### Negative -- Leiden implementations in Rust are less mature than Louvain's. Vendoring ~400 LoC or depending on a possibly-young crate is real implementation risk. Mitigation: the fallback exists specifically for this. +- Leiden implementations in Rust are less mature than simpler local graph cuts. Vendoring ~400 LoC or depending on a possibly-young crate is real implementation risk. Mitigation: the weighted-components fallback exists specifically for this. - Modularity is a quality *signal* not a hard threshold. Weak clusterings ship. Operators reading `CLA-FACT-CLUSTERING-WEAK-MODULARITY` may not know how to act on it. Mitigation: v0.2 validation work (and the C1 cost-model spike) clarifies whether a hard threshold is warranted. - Module-level only. Classes, functions, and decorators don't get their own clusters in v0.1. Operators wanting finer grains (sub-module clusters) get the "module is the unit" limitation — noted in release documentation. ### Neutral -- Algorithm selection is a config, not a code change. Switching from Leiden to Louvain mid-project (if a critical implementation bug emerges) is a `clarion.yaml` edit + reindex. +- Algorithm selection is a config, not a code change. Switching from Leiden to weighted-components mid-project is a `clarion.yaml` edit + reindex. - Resolution parameter (`γ`) is exposed for operators with unusual codebases; most never touch it. - Subsystem entity IDs are content-addressed over sorted member IDs; renaming a module changes the hash. This is correct — "the subsystem" changed composition, so a new identity is right. Filigree issues tagged to the old ID follow the ADR-003 EntityAlias story. diff --git a/docs/clarion/adr/ADR-018-identity-reconciliation.md b/docs/clarion/adr/ADR-018-identity-reconciliation.md index dbf3fadb..aa6cb288 100644 --- a/docs/clarion/adr/ADR-018-identity-reconciliation.md +++ b/docs/clarion/adr/ADR-018-identity-reconciliation.md @@ -16,7 +16,7 @@ Three identity schemes coexist and none are byte-equal for the same underlying s | Scheme | Example | Owner | Format | |---|---|---|---| | Clarion `EntityId` | `python:class:auth.tokens::TokenManager` | Clarion | `{plugin_id}:{kind}:{canonical_qualified_name}` | -| Wardline `qualname` | `TokenManager.verify` | Wardline `FingerprintEntry` | Nested class/method dotted form (not Python `__qualname__`; no `` suffix) | +| Wardline `module` + `qualified_name` | `src/auth/tokens.py` + `TokenManager.verify` | Wardline `FingerprintEntry` | Source file path plus Python's bare `__qualname__`; not byte-equal to Clarion's dotted-module-prefixed `qualified_name` | | Wardline exception-register `location` | `src/wardline/scanner/engine.py::ScanEngine._scan_file` | `wardline.exceptions.json` | `{file_path}::{qualname}` | Any cross-tool query — "which Filigree findings attach to this Clarion entity?", "which Wardline exception covers this qualname?" — has to bridge at least two of these. The ADR-003 decision to use symbolic canonical names produces Clarion's scheme but leaves the translation question open. @@ -32,12 +32,34 @@ The 2026-04-17 panel's doctrine synthesis (`11-doctrine-panel-synthesis.md`) fla ### Translation direction and authority - **Inbound translation only.** Clarion translates Wardline qualnames, exception-register locations, and SARIF logical locations into `EntityId`s. Clarion does not push its ID scheme outbound — Wardline's emissions remain in Wardline's format, and Clarion's translation layer maps them at ingest. -- **Wardline is authoritative for its own qualnames.** `FingerprintEntry.qualname` is Wardline's contract; Clarion reads it and maps it. A future Wardline refactor that changes qualname format is a Wardline-side decision Clarion adapts to; the inverse is not true. +- **Wardline is authoritative for its own qualnames.** `FingerprintEntry.qualified_name` and its paired `module` path are Wardline's contract; Clarion reads them and maps them. A future Wardline refactor that changes either field's format is a Wardline-side decision Clarion adapts to; the inverse is not true. - **Reverse mapping is recorded, not pushed.** `WardlineMeta.wardline_qualname` on each Clarion entity property is the reverse lookup cache. It lives on Clarion's entity, not on Wardline's side, and is re-computed on every `clarion analyze`. +### 2026-05-18 amendment: asymmetric qualname storage is canonical + +Sprint 1 verification proved that the two products encode the same Python symbol +with different field boundaries: + +- Clarion's Python plugin emits `qualified_name = + "{dotted_module}.{python.__qualname__}"` on each entity, e.g. + `auth.tokens.TokenManager.verify`. +- Wardline's `FingerprintEntry` stores `module` as the source file path and + `qualified_name` as Python's bare `__qualname__`, e.g. + `src/auth/tokens.py` plus `TokenManager.verify`. + +Direct string equality between Clarion's `qualified_name` and Wardline's +`qualified_name` is therefore forbidden for joins. Wardline-to-Clarion +translation composes Clarion's dotted module name from Wardline's `module` +using the same rules as the Python plugin's `module_dotted_name()` (`src/` +prefix stripped, `.py` removed, and `__init__.py` collapsed), then appends +Wardline's bare `qualified_name`. Clarion-to-Wardline translation must prefer +the recorded `WardlineMeta` / translator output; naively splitting on dots is +unsafe because dotted class chains and `` markers are part of Python's +`__qualname__`, not the module path. + ### Translation entry points (v0.1) -1. **`wardline.fingerprint.json`**: for each `FingerprintEntry`, compute `(file_path, qualname) → EntityId` using Wardline's `module_file_map` (from `ScanContext`). Write `WardlineMeta.wardline_qualname = qualname` on the resolved Clarion entity. +1. **`wardline.fingerprint.json`**: for each `FingerprintEntry`, compute `(module, qualified_name) → EntityId` using Wardline's `module_file_map` (from `ScanContext`). Write `WardlineMeta.wardline_qualname = qualified_name` on the resolved Clarion entity. 2. **`wardline.exceptions.json`**: parse `location` as `file_path::qualname` (split on the first `::`); same mapping rule. Unresolvable entries emit `CLA-INFRA-WARDLINE-EXCEPTION-UNRESOLVED` and persist as dangling records with `entity_id: null`. 3. **`wardline.sarif.baseline.json`**: use `location.logicalLocations[].fullyQualifiedName` when present, or `partialFingerprints` as a fallback. Unresolvable SARIF results carry `metadata.clarion.unresolved: true` through translation. 4. **`GET /api/v1/entities/resolve?scheme=&value=`**: HTTP read-API oracle. Schemes accepted: `wardline_qualname`, `wardline_exception_location`, `file_path`, `sarif_logical_location`. Response carries `resolution_confidence` (`exact | heuristic | none`) plus candidates for non-exact matches. 404-like misses return 200 with `resolution_confidence: "none"` to distinguish "Clarion doesn't know" from "Clarion is down." @@ -65,7 +87,7 @@ This preserves the federation test: removing Wardline breaks Wardline-derived an ### Alternative 1: Wardline adopts Clarion's entity-ID scheme -Wardline changes its `FingerprintEntry.qualname` to carry Clarion's `{plugin_id}:{kind}:{canonical_qualified_name}` format directly. +Wardline changes its `FingerprintEntry.qualified_name` to carry Clarion's `{plugin_id}:{kind}:{canonical_qualified_name}` format directly. **Pros**: zero translation layer; one identity scheme across the suite; cross-tool queries are string-equal comparisons. diff --git a/docs/clarion/adr/ADR-024-guidance-schema-vocabulary.md b/docs/clarion/adr/ADR-024-guidance-schema-vocabulary.md index 06849d08..9c4398d5 100644 --- a/docs/clarion/adr/ADR-024-guidance-schema-vocabulary.md +++ b/docs/clarion/adr/ADR-024-guidance-schema-vocabulary.md @@ -92,7 +92,7 @@ The semantic ordering `project → subsystem → package → module → class ### `findings.run_id` ↔ `runs.id` relationship -This ADR confirms (does not change) that `findings.run_id` and `runs.id` are the same string. The schema does not enforce it via foreign key (see filigree issue F-17, follow-up); confirming it here so future readers do not have to derive it from code. The Rust writer-actor produces both identifiers from the same `Uuid::new_v4()` per analyze invocation. +This ADR confirms that `findings.run_id` and `runs.id` are the same string. The Rust writer-actor produces both identifiers from the same `Uuid::new_v4()` per analyze invocation. The Sprint 2 F-17 follow-up encoded that provenance relationship mechanically: `findings.run_id` now references `runs(id)` in `0001_initial_schema.sql`. ## Alternatives Considered diff --git a/docs/clarion/adr/ADR-030-on-demand-summary-scope.md b/docs/clarion/adr/ADR-030-on-demand-summary-scope.md index 9b530c03..ae506779 100644 --- a/docs/clarion/adr/ADR-030-on-demand-summary-scope.md +++ b/docs/clarion/adr/ADR-030-on-demand-summary-scope.md @@ -49,7 +49,7 @@ A future operator may want to prewarm summaries for a subset of the project (hig Hierarchical aggregation requires: -- A clustering pass (ADR-006 / WP4 Phase 3 — Leiden / Louvain). Deferred to v0.2 by the scope-amendment memo. +- A clustering pass (ADR-006 / ADR-032 / WP4 Phase 3 — Leiden / weighted-components). Deferred to v0.2 by the scope-amendment memo. - A determinate ordering for aggregation (Phase 8's entity-set diff — deferred). - An aggregation prompt that handles entity-count variability per module/subsystem. diff --git a/docs/clarion/adr/ADR-031-schema-validation-policy.md b/docs/clarion/adr/ADR-031-schema-validation-policy.md new file mode 100644 index 00000000..b742c57a --- /dev/null +++ b/docs/clarion/adr/ADR-031-schema-validation-policy.md @@ -0,0 +1,426 @@ +# ADR-031: Schema-Validation Policy for Enum-Shaped TEXT Columns + +**Status**: Accepted +**Date**: 2026-05-18 +**Deciders**: qacona@gmail.com +**Context**: F-13 from the 2026-05-03 skeleton audit observed that the +`0001_initial_schema.sql` migration carries six enum-shaped `TEXT` columns +without `CHECK` constraints, while two sibling columns in the same migration +do (`edges.confidence`, `summary_cache.stale_semantic`). The divergence is +unprincipled and undocumented. ADR-024 § Consequences/Neutral named F-13 as +out-of-scope for that ADR and deferred a policy decision here. Triggered by +filigree issue `clarion-fbe50aa6e1` (P2). + +## Summary + +Schema-level `CHECK` constraints are required on enum-shaped `TEXT` columns +whose vocabulary is **closed and core-owned**, and forbidden on columns whose +vocabulary is **plugin-extensible** (ADR-022). For v0.1 this means +`findings.{kind, severity, status}` and `runs.status` gain `CHECK` clauses +matching the values defined in ADR-004, ADR-017, and the `RunStatus` Rust +enum; `entities.kind` and `edges.kind` do **not** receive `CHECK` clauses +because ADR-022 reserves edge-kind and entity-kind vocabulary to the plugin +manifest. The writer-actor (per ADR-011) remains the canonical normal-path +validator — typed Rust enums at the command boundary (`commands.rs`) and +`enforce_edge_contract` (`writer.rs:411`) prevent bad values from reaching +the SQL layer. `CHECK` constraints are defense-in-depth: they catch +hand-typed string literals in writer-actor code (e.g., `'running'` at +`writer.rs:322`), accidental drift when a Rust enum gains a variant without +a schema update, and any future debugging path that bypasses the writer +(`sqlite3` CLI, repair scripts). The two-layer model is the same shape as +`edges.confidence` already uses; ADR-031 generalises that precedent to a +documented policy. Migration `0001_initial_schema.sql` is edited in place +under the ADR-024 in-place edit policy (no external consumers exist). + +## Context + +The 2026-05-03 skeleton-audit reviewer additions flagged F-13: + +> Enum-typed `TEXT` columns lack `CHECK` constraints (`entities.kind`, +> `edges.kind`, `findings.{kind,severity,status}`, `runs.status`); +> validation lives in the writer-actor by design but the policy is +> undocumented. + +The audit deferred a fix to its own ADR. The motivating bug — +`clarion-4cd11905e2`, closed by ADR-024 — was the priority-affinity slip +where a TEXT-affinity column silently accepted any string the writer +inserted. The audit's framing was that one closed bug was the *first +instance* of a class; every enum-shaped TEXT column carries the same latent +defect until the policy is named. + +Two in-house precedents already use `CHECK`: + +- `edges.confidence` (`0001_initial_schema.sql:80-81`) — `CHECK (confidence + IN ('resolved', 'ambiguous', 'inferred'))`, per ADR-028. +- `summary_cache.stale_semantic` (`0001_initial_schema.sql:134`) — `CHECK + (stale_semantic IN (0, 1))`. + +Both columns have closed, core-owned vocabularies. Both are defended by +typed Rust types (`EdgeConfidence`, `bool`) at the writer boundary. The +existence of the CHECK on `edges.confidence` two lines above `edges.kind` +(which has no CHECK) is the visual evidence that the project's *intended* +policy is defense-in-depth — the policy was just never written down, so the +treatment is inconsistent. + +The columns flagged by F-13 split into two categories: + +1. **Closed, core-owned vocabulary** (CHECK applies): + - `findings.kind` — `defect | fact | classification | metric | suggestion` + (5 values, ADR-004 + `detailed-design.md:275`). + - `findings.severity` — `INFO | WARN | ERROR | CRITICAL | NONE` + (5 values, ADR-017). + - `findings.status` — `open | acknowledged | suppressed | promoted_to_issue` + (4 values, `detailed-design.md:295`). + - `runs.status` — `running | skipped_no_plugins | completed | failed` + (4 values; the three terminal states are the `RunStatus` enum in + `commands.rs:26`; `'running'` is the in-flight literal inserted at + `writer.rs:322` during `BeginRun`). + +2. **Plugin-extensible vocabulary** (CHECK does not apply): + - `entities.kind` — plugin-declared per ADR-022 §"Plugin owns + (ontology-vocabulary)". Core enforces only the identifier grammar + `[a-z][a-z0-9_]*` and the three reserved-kind names; the universe of + valid kinds is unbounded. + - `edges.kind` — also plugin-declared per ADR-022. The current writer + (`writer.rs:394-401`) hardcodes a 9-value ontology for the v0.1 + Python-plugin shape, but ADR-022 §"Plugin owns" explicitly admits + plugin-declared edge kinds beyond the four core-reserved structural + ones. A schema-level CHECK would over-constrain the data layer + against ADR-022's contract. + +The non-flagged columns (e.g., `edges.confidence`, `summary_cache +.stale_semantic`) are already CHECK-protected and remain so. + +`findings` is not yet written by any Sprint-1 or Sprint-2 code — the table +is forward-defined for WP4+. The CHECK additions to `findings` are +zero-blast-radius today; they become the schema invariant the first WP4 PR +will encode against. + +## Decision + +### Policy + +A migration must include a `CHECK (column IN (...))` constraint on every +`TEXT` column whose value set is **closed and core-owned**. A migration +must **not** include a `CHECK` constraint on a `TEXT` column whose value +set is plugin-declared (ADR-022). Numeric enum-shaped columns (e.g., +`summary_cache.stale_semantic`) follow the same rule: closed → CHECK, +extensible → no CHECK. + +"Closed and core-owned" means: the complete value set is enumerated in an +Accepted ADR or in a core-owned Rust type (`enum` plus, if applicable, +the small set of string literals the writer uses for in-flight states). +Adding or renaming a value requires both an ADR (or ADR amendment) and +a paired migration update. + +"Plugin-extensible" means: a plugin's startup manifest contributes +values per ADR-022 (§"Plugin owns"), and the universe of valid values is +not knowable at schema-creation time. + +### v0.1 application + +Migration `0001_initial_schema.sql` is edited in place under the +ADR-024 in-place edit policy (retirement trigger remains: first +external operator pulling a published Clarion build). The following +CHECK clauses are added: + +| Column | CHECK clause | Source of truth | +|---|---|---| +| `findings.kind` | `CHECK (kind IN ('defect', 'fact', 'classification', 'metric', 'suggestion'))` | [ADR-004](./ADR-004-finding-exchange-format.md), `detailed-design.md:275` | +| `findings.severity` | `CHECK (severity IN ('INFO', 'WARN', 'ERROR', 'CRITICAL', 'NONE'))` | [ADR-017](./ADR-017-severity-and-dedup.md) | +| `findings.status` | `CHECK (status IN ('open', 'acknowledged', 'suppressed', 'promoted_to_issue'))` | `detailed-design.md:295` | +| `runs.status` | `CHECK (status IN ('running', 'skipped_no_plugins', 'completed', 'failed'))` | [ADR-011](./ADR-011-writer-actor-concurrency.md), `commands.rs:26` (`RunStatus`) + `writer.rs:322` (`'running'` literal) | + +No CHECK is added to `entities.kind` or `edges.kind`. The schema comment +on each of those columns is updated to point at this ADR so a future +reader does not re-litigate the omission. + +### Validation layers + +The defense-in-depth model is two layers: + +1. **Layer A — Writer-actor typed API (primary).** The writer-actor's + command boundary (`commands.rs` `WriterCmd`, `RunStatus`, + `EdgeConfidence`, the forthcoming `FindingKind`/`FindingSeverity`/ + `FindingStatus` enums when WP4 lands) constructs valid SQL values + from typed Rust enums. `enforce_edge_contract` (`writer.rs:411`) is + the additional per-kind contract layer for `edges`. This layer + prevents bad values from being inserted in normal use; it produces + structured `StorageError::WriterProtocol` errors with `CLA-INFRA-*` + codes that surface in `runs.stats.failure_reason`. + +2. **Layer B — SQL CHECK constraints (defense).** SQLite enforces the + CHECK clauses on every write that reaches the SQL layer, regardless + of which code path emitted it. Bad values produce + `SQLITE_CONSTRAINT_CHECK` errors. This catches: + - Hand-typed string literals in writer-actor code where a fat-finger + bypasses the typed API (e.g., `INSERT ... VALUES (..., 'runing')` + misspelling `'running'`). + - Rust enum drift: a new `RunStatus` variant added without updating + the CHECK list raises `SQLITE_CONSTRAINT_CHECK` at the first write, + making the omission self-reporting at test time. + - Out-of-band writes from `sqlite3` CLI debugging or future repair + scripts. + - Test-only paths that construct rows by raw SQL rather than through + the writer. + +### Test layer + +The schema-apply test suite (`crates/clarion-storage/tests/schema_apply.rs`) +already asserts CHECK rejection on `edges.confidence` (test +`edges_confidence_column_rejects_unknown_tier` at line 538). This ADR adds +parallel rejection tests for each of the four newly CHECK-constrained +columns (`findings.{kind, severity, status}`, `runs.status`). The pattern +is: insert a row with a deliberately invalid value, assert the error +message contains `"CHECK constraint failed"`. Adding a new valid value +without updating both the CHECK clause and these tests will fail CI. + +The writer-actor tests (`crates/clarion-storage/tests/writer_actor.rs`) +already exercise the Layer-A typed enums on the runs.status side +(`RunStatus::Completed`, `RunStatus::Failed`); no change required there. + +### Schema-comment discipline + +Each CHECK-constrained column gets a short SQL comment naming this ADR +and the source-of-truth ADR for its vocabulary: + +```sql +status TEXT NOT NULL + -- ADR-031: closed vocabulary; values from ADR-011 + RunStatus + CHECK (status IN ('running', 'skipped_no_plugins', 'completed', 'failed')), +``` + +Each non-CHECK enum-shaped column (`entities.kind`, `edges.kind`) gets a +short SQL comment naming this ADR and the reason: + +```sql +kind TEXT NOT NULL, + -- ADR-031: plugin-extensible vocabulary (ADR-022); no CHECK by policy +``` + +The comments are the future-reader's first stop; without them the +non-uniform CHECK treatment looks like an oversight. + +### Out of scope + +This ADR does not address: + +- The five remaining audit findings (F-14 through F-17 plus F-13 + itself) — each is a distinct schema concern with its own filigree + issue (`clarion-ef9bd365bf`, `clarion-fb1b8fb5a0`, + `clarion-523b2eebad`, `clarion-ba198ee96b`). +- JSON-shape validation on `properties`, `config`, `stats`, `evidence`, + `related_entities`, `supports`, `supported_by` columns. These are + TEXT-typed JSON blobs whose shape is owned by the writer-actor and + validated (where validated at all) at the typed-Rust boundary. CHECK + constraints on JSON shape are not a SQLite primitive and out of + scope here; the policy is silent on them. +- `confidence_basis` and `suppression_reason` on `findings` — both are + free-text fields with no enumerated vocabulary; no CHECK applies. + +### When the policy switches + +The policy switches from "edit `0001` in place" to "stack `0002_*.sql`" +at the same retirement trigger as ADR-024: the first time any external +operator pulls a published Clarion build and produces a +`.clarion/clarion.db`. After that point, vocabulary expansions for any +CHECK-constrained column require a stacked migration that rewrites the +table (SQLite cannot `ALTER TABLE ... DROP CHECK`; the canonical workaround +is the [SQLite "make other kinds of table schema changes" recipe](https://www.sqlite.org/lang_altertable.html#otheralter) +— rename, create new, copy, drop old, rename new — inside a single +transaction). Pre-trigger, the in-place edit is the lower-debt path. + +## Alternatives Considered + +### Alternative 1: No CHECK constraints anywhere; writer-actor is the only validator + +Document explicitly that `CHECK` is not used; writer-actor is the sole +truth and tests assert writer-actor validation paths. Remove the existing +`edges.confidence` CHECK to make the policy uniform. + +**Pros**: the simplest possible mental model — "validation lives in the +writer, full stop." No two-layer story to maintain. Schema migrations are +mechanical and never need a "what's the closed vocabulary today" check. + +**Cons**: throws away free defense-in-depth. The `'running'` literal at +`writer.rs:322` is exactly the kind of typo a CHECK catches that the +writer-actor cannot — the typed `RunStatus` enum has no `Running` variant +(in-flight state is intentionally outside the terminal-status enum), so +the literal is hand-typed. A misspelling there would silently insert +`'runing'` into `runs.status`, and downstream queries filtering on +`status = 'running'` would silently miss the run. Tests would only catch +this if they happened to read back the status string. The CHECK closes +that hole at zero ongoing cost. + +Removing the existing `edges.confidence` and `summary_cache.stale_semantic` +CHECKs would be a net loss in confidence with no compensating gain. The +audit's framing also pushes the other way: "validation policy undocumented" +is the bug; the answer "we don't validate at all" preserves the documented +fix but loses the existing protection. + +**Why rejected**: removes working defense for ideological uniformity. + +### Alternative 2: CHECK everything, including `entities.kind` and `edges.kind`, with a "registered kinds" mechanism + +Add `CHECK` on `entities.kind` and `edges.kind` against a `registered_kinds` +lookup table populated at plugin-startup time. Manifest-declared kinds +land in `registered_kinds` before any insert; the CHECK becomes +`CHECK (kind IN (SELECT kind FROM registered_kinds))`. + +**Pros**: uniform "every enum-shaped TEXT column has a CHECK" policy. No +exception for plugin-extensible vocabulary. + +**Cons**: SQLite CHECK constraints cannot reference other tables (per +documentation — CHECK expressions are evaluated against the current row +only and may not contain subqueries). A foreign key would work, but a +foreign key on `kind` to `registered_kinds(kind)` requires `kind` to be +unique in `registered_kinds`, which is fine, but the FK then forbids +deleting a `registered_kinds` row while any entity uses it — a startup +ordering nightmare when plugins change between runs. The mechanism is also +heavier than the threat: ADR-022 already enforces manifest-declared kinds +at the `analyze_file` notification boundary (`CLA-INFRA-PLUGIN-UNDECLARED-KIND` +in the writer-actor and in the host's emission-acceptance check). Adding a +data-layer enforcement of a property the protocol layer already enforces +is duplicated work that lands in the wrong place. + +**Why rejected**: SQLite CHECK + plugin-extensibility is fundamentally +mismatched; the protocol-layer enforcement is already there. + +### Alternative 3: CHECK only where the column is read in a `WHERE` clause + +Add CHECK constraints only where a query path discriminates on the +column value (e.g., `WHERE status = 'failed'`); skip CHECKs on columns +whose enum values are only read back, never filtered on. + +**Pros**: scopes the defense to where wrong values can produce wrong +results (silent filter mismatches), not where wrong values just look +wrong on inspection. + +**Cons**: requires a query-surface audit every time a CHECK decision is +made, which is brittle as the codebase grows. The audit becomes a CHECK +decision at PR-review time, not at schema-design time. The mental cost +of "is this column filtered on?" is bigger than the mental cost of "is +this vocabulary closed?" — and the answer to the second question is +already in an ADR. + +**Why rejected**: the policy needs to be cheap to apply, not +optimisation-driven. + +### Alternative 4: Defer to v0.2; comment the current schema with TODO links to this audit + +Skip the schema edit; document the policy gap; add CHECKs when WP4 lands +findings writes and the value sets are exercised against real data. + +**Pros**: no Sprint-2 churn for forward-looking columns nobody is writing +to yet. The risk is theoretical until WP4 writes findings. + +**Cons**: ADR-024 explicitly named this issue as deferred to its own ADR; +deferring further moves the decision into the same "implicit-policy" +state ADR-031 is trying to retire. The `runs.status` and `entities.kind` +columns *are* being written today, and the audit's "same class of bug +will appear on every enum-typed TEXT column" framing argues against +waiting for the first WP4 instance. + +The other cost of deferral: ADR-024 set the precedent that schema +corrections happen in place before external consumers exist; ADR-031 +is well-positioned to use that policy now. Once the in-place trigger +fires, every CHECK addition costs a stacked migration with the +SQLite table-rebuild recipe. + +**Why rejected**: the cheap window is now; the deferral cost is +permanent. + +## Consequences + +### Positive + +- The same-shape question that the audit framed as a class of bugs is + answered uniformly at the schema layer. The next reader of + `0001_initial_schema.sql` sees the CHECK + comment pattern and does + not have to reconstruct the policy from precedent. +- Defense-in-depth on `runs.status` catches a real typo class: hand-typed + string literals in writer-actor code (the `'running'` and `'failed'` + literals at four sites in `writer.rs`). The `RunStatus` enum prevents + most of these, but not the in-flight `'running'` insert. +- WP4 (findings emission) lands against a schema whose CHECK clauses + already encode the ADR-004 and ADR-017 vocabularies. The schema + becomes the executable specification; WP4's `FindingKind` / + `FindingSeverity` / `FindingStatus` Rust enums must agree with it by + CI construction. +- The `entities.kind` / `edges.kind` exceptions are documented at the + schema-comment level, so a future "should we add CHECKs to these?" + proposal is answered in place by the comment + this ADR, not by + re-reading ADR-022 and inferring. +- The two existing CHECK precedents (`edges.confidence`, + `summary_cache.stale_semantic`) are now backed by a written policy + they exemplify, not by accident. + +### Negative + +- Schema-level vocabulary additions become a two-step edit: the ADR + (or amendment) updates the vocabulary, then the schema migration + updates the CHECK clause. Pre-trigger this is one in-place edit; + post-trigger this is a stacked migration with the table-rebuild + recipe. Migration-author docs need to flag this — the cost is small + per edit but real, and the table-rebuild recipe is verbose. +- A misspelled value in a writer-actor hand-typed literal becomes a + `SQLITE_CONSTRAINT_CHECK` failure at runtime rather than a silent + insert. This is the *intended* behaviour but it shifts the failure + mode from "data quietly wrong" to "run fails." Either path requires + test coverage; the new path is louder. +- The schema comments add 8–10 lines to `0001_initial_schema.sql`. The + file grows slightly; readability improves on net. + +### Neutral + +- The writer-actor remains the canonical Layer-A validator; the CHECK + clauses do not change its role. The `enforce_edge_contract` function + and the `RunStatus` typed enum continue to be the normal-path + enforcement; the CHECK is the safety net. +- Properties / config / stats / evidence JSON columns are out of scope + here. Their validation story (if any) belongs to a separate decision + about JSON-schema enforcement at the writer or pre-flight layer. + +## Related Decisions + +- [ADR-011](./ADR-011-writer-actor-concurrency.md) — names the writer-actor + as the canonical mutation path; this ADR generalises its validation + authority into a documented two-layer model. +- [ADR-022](./ADR-022-core-plugin-ontology.md) — defines plugin authority + over `entities.kind` and `edges.kind`. This ADR honours that boundary by + *not* adding CHECK constraints to those columns. +- [ADR-024](./ADR-024-guidance-schema-vocabulary.md) — established the + in-place edit policy for `0001_initial_schema.sql` and named the + retirement trigger; this ADR uses the same policy and refers to the + same trigger. ADR-024 § Consequences/Neutral also explicitly named F-13 + as deferred to a follow-up ADR — this one. +- [ADR-028](./ADR-028-edge-confidence-tiers.md) — defines the + `edges.confidence` vocabulary that the existing CHECK constraint + encodes; the in-house precedent ADR-031 generalises. +- [ADR-004](./ADR-004-finding-exchange-format.md) — the source of truth for + `findings.kind` and `findings.status` values. +- [ADR-017](./ADR-017-severity-and-dedup.md) — the source of truth for + `findings.severity` values (and the `internal_severity` round-trip slot + that preserves them across Filigree). + +## References + +- [Skeleton audit](../../superpowers/handoffs/2026-05-03-skeleton-audit.md) + — F-13 in the Reviewer additions table; the audit framing that + motivated this ADR. +- `crates/clarion-storage/migrations/0001_initial_schema.sql:80-81, 134` + — the two existing CHECK precedents this ADR generalises. +- `crates/clarion-storage/src/commands.rs:26-43` — `RunStatus` Rust enum; + the typed Layer-A validator for `runs.status` writes. +- `crates/clarion-storage/src/writer.rs:322` — the `'running'` hand-typed + literal at `BeginRun`; the kind of fat-finger the CHECK catches. +- `crates/clarion-storage/src/writer.rs:411` — `enforce_edge_contract`, + the Layer-A validator for `edges` writes. +- `crates/clarion-storage/tests/schema_apply.rs:538` — + `edges_confidence_column_rejects_unknown_tier`, the test pattern this + ADR's tests follow. +- Filigree issue `clarion-fbe50aa6e1` — the audit issue this ADR closes. +- [SQLite documentation: CHECK constraints](https://www.sqlite.org/lang_createtable.html#ckconst) + and [Making Other Kinds of Table Schema Changes](https://www.sqlite.org/lang_altertable.html#otheralter) + — the SQL semantics this ADR relies on, and the post-trigger + table-rebuild recipe that future CHECK changes will use. diff --git a/docs/clarion/adr/ADR-032-weighted-components-clustering-fallback.md b/docs/clarion/adr/ADR-032-weighted-components-clustering-fallback.md new file mode 100644 index 00000000..bf215542 --- /dev/null +++ b/docs/clarion/adr/ADR-032-weighted-components-clustering-fallback.md @@ -0,0 +1,54 @@ +# ADR-032: Weighted-Components Clustering Fallback Naming + +**Status**: Accepted +**Date**: 2026-05-18 +**Deciders**: qacona@gmail.com +**Context**: Phase 3 landed with a deterministic fallback implementation that groups modules by connected components over high-weight edges, but ADR-006 and the public config name called it Louvain. + +## Summary + +Clarion v0.1 keeps Leiden as the default Phase 3 clustering algorithm. The +fallback algorithm is named `weighted_components`, not `louvain`, because the +implementation does not perform Louvain modularity optimisation. The config +surface is: + +```yaml +analysis: + clustering: + algorithm: weighted_components +``` + +Subsystem `properties_json.algorithm`, MCP subsystem envelopes, and +`runs.stats.clustering.algorithm` record `weighted_components` when this +fallback supplies the partition. `runs.stats.clustering.configured_algorithm` +records the requested config value for auditability. + +When the configured algorithm is `leiden`, the fallback trigger is explicit: +Clarion computes `weighted_components` if Leiden returns zero or one community, +and uses the fallback only when it produces more communities than Leiden. + +## Decision + +Rename the local fallback from Louvain to weighted-components before v0.1 +publishes stored subsystem rows. The fallback: + +- treats the module dependency graph as an undirected graph for local grouping; +- computes the average positive edge weight; +- keeps edges whose weight is at least that threshold; +- emits connected components whose size is at least `min_cluster_size`. + +This is a deterministic, explainable local cut. It is not Louvain, and must not +be reported as Louvain in config, stored properties, stats, or MCP output. + +## Consequences + +- `analysis.clustering.algorithm` supports `leiden` and `weighted_components`. +- A run configured as `leiden` can persist `weighted_components` in subsystem + properties and run stats when the auto-fallback trigger fires. +- Existing pre-v0.1 artifacts that recorded `louvain` should be regenerated or + treated as pre-publish test data. +- A future real Louvain implementation remains allowed, but must land as a new + algorithm value with tests and ADR coverage. +- ADR-006 remains authoritative for the Leiden default, module graph, output + shape, and weak-modularity reporting. This ADR amends only the fallback + implementation name and behavior. diff --git a/docs/clarion/adr/README.md b/docs/clarion/adr/README.md index abb0e276..f0390d5f 100644 --- a/docs/clarion/adr/README.md +++ b/docs/clarion/adr/README.md @@ -11,7 +11,7 @@ This folder is the canonical home for authored Clarion architecture decision rec | [ADR-003](./ADR-003-entity-id-scheme.md) | Entity ID scheme: symbolic canonical names | Accepted | | [ADR-004](./ADR-004-finding-exchange-format.md) | Finding-exchange format: Filigree-native intake | Accepted | | [ADR-005](./ADR-005-clarion-dir-tracking.md) | `.clarion/` git-committable by default; DB included, run logs excluded | Accepted | -| [ADR-006](./ADR-006-clustering-algorithm.md) | Clustering algorithm — Leiden on imports+calls subgraph; Louvain fallback | Accepted | +| [ADR-006](./ADR-006-clustering-algorithm.md) | Clustering algorithm — Leiden on imports+calls subgraph; fallback amended by ADR-032 | Accepted; amended | | [ADR-007](./ADR-007-summary-cache-key.md) | Summary cache key — 5-part composite with TTL backstop and churn-eager invalidation | Accepted | | [ADR-011](./ADR-011-writer-actor-concurrency.md) | Writer-actor concurrency with per-N-files transactions; `--shadow-db` opt-in | Accepted | | [ADR-012](./ADR-012-http-auth-default.md) | HTTP read-API authentication — UDS default with token fallback | Accepted | @@ -31,6 +31,8 @@ This folder is the canonical home for authored Clarion architecture decision rec | [ADR-028](./ADR-028-edge-confidence-tiers.md) | Edge confidence tiers (`resolved` / `ambiguous` / `inferred`); MCP queries default to `>= resolved`; inferred edges lazy-computed at query time | Accepted | | [ADR-029](./ADR-029-entity-associations-binding.md) | Entity associations — Filigree-side `entity_associations` table; `add_entity_association` MCP tool on Filigree; `issues_for` MCP tool on Clarion; WP9 split into A (binding, v0.1) and B (findings emission) | Accepted | | [ADR-030](./ADR-030-on-demand-summary-scope.md) | On-demand summary scope — narrows WP6 to MCP-driven `summary(id)`; 5-tuple cache key unchanged; module/subsystem aggregation deferred to v0.2 | Accepted | +| [ADR-031](./ADR-031-schema-validation-policy.md) | Schema-validation policy — CHECK on closed core-owned vocabularies (`findings.{kind,severity,status}`, `runs.status`); writer-actor + manifest are the only enforcement layer for plugin-extensible vocabularies (`entities.kind`, `edges.kind`) | Accepted | +| [ADR-032](./ADR-032-weighted-components-clustering-fallback.md) | Weighted-components clustering fallback naming | Accepted | ## Backlog still tracked in the detailed design diff --git a/docs/clarion/v0.1/detailed-design.md b/docs/clarion/v0.1/detailed-design.md index a29eaff0..4fb249eb 100644 --- a/docs/clarion/v0.1/detailed-design.md +++ b/docs/clarion/v0.1/detailed-design.md @@ -250,7 +250,6 @@ struct Entity { ```rust struct Edge { - id: EdgeId, // deduped hash of (kind, from, to) from: EntityId, to: EntityId, kind: String, // plugin-defined OR core-reserved @@ -259,6 +258,15 @@ struct Edge { } ``` +**Edge identity and coexistence policy**: the store admits at most one edge for a +given `(kind, from_id, to_id)` tuple. `properties` carries evidence and +kind-specific metadata (for example ambiguous-call candidates), but it is not +part of edge identity and does not allow multiple same-kind relationships +between the same endpoints to coexist. Re-analysis and repeated plugin evidence +therefore remain idempotent; callers that need several observations for one +relationship must merge them into the single edge's properties shape rather than +emitting duplicate rows. + **Core-reserved edge kinds**: `contains`, `guides`, `emits_finding`, `in_subsystem`. All others are plugin-defined. ### Finding (Rust) @@ -586,7 +594,7 @@ The v0.2 **Wardline annotation descriptor** (§9, promoted from earlier deferral ### SQLite rationale -- Graph algorithms (Louvain, Leiden, centrality, path-finding) run in Rust against in-memory projections; the store serves neighbour lookups. +- Graph algorithms (Leiden, weighted-components fallback, centrality, path-finding) run in Rust against in-memory projections; the store serves neighbour lookups. - Consult-mode queries are overwhelmingly one-hop (callers, callees, contains) — indexed range scans. - WAL mode with a **writer-actor** (single owner of the write connection; see Concurrency below) permits `clarion serve` to keep answering reads while `clarion analyze` is ingesting and while consult-mode cache writes happen. - JSON1 handles plugin property bags without giving up query ergonomics. @@ -633,37 +641,49 @@ CREATE INDEX ix_entities_content_hash ON entities(content_hash); -- Tags (denormalised) CREATE TABLE entity_tags ( + -- `plugin_id` is the namespace that emitted/owns the free-form tag. + -- Entity IDs already carry an entity owner, but multiple plugins may tag + -- the same core or sibling entity; tag ownership is therefore explicit. entity_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, + plugin_id TEXT NOT NULL, tag TEXT NOT NULL, - PRIMARY KEY (entity_id, tag) + PRIMARY KEY (entity_id, plugin_id, tag) ); CREATE INDEX ix_entity_tags_tag ON entity_tags(tag); +CREATE INDEX ix_entity_tags_plugin_tag ON entity_tags(plugin_id, tag); --- Edges. Deduped by (kind, from_id, to_id) — two edges of the same kind --- between the same entities collapse into one (the plugin's emitter --- may observe a call twice for overloaded names; the store is idempotent). +-- Edges. Natural PK (kind, from_id, to_id) per ADR-026: two edges of the +-- same kind between the same entities collapse into one even when their +-- properties differ. The properties bag is evidence/metadata, not identity. CREATE TABLE edges ( - id TEXT PRIMARY KEY, - kind TEXT NOT NULL, - from_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, - to_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, - properties TEXT, - source_file_id TEXT REFERENCES entities(id), + kind TEXT NOT NULL, + from_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, + to_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, + properties TEXT, + source_file_id TEXT REFERENCES entities(id), source_byte_start INTEGER, - source_byte_end INTEGER, - UNIQUE (kind, from_id, to_id) -); -CREATE INDEX ix_edges_from_kind ON edges(from_id, kind); -CREATE INDEX ix_edges_to_kind ON edges(to_id, kind); -CREATE INDEX ix_edges_kind ON edges(kind); + source_byte_end INTEGER, + confidence TEXT NOT NULL DEFAULT 'resolved' + CHECK (confidence IN ('resolved', 'ambiguous', 'inferred')), + PRIMARY KEY (kind, from_id, to_id) +) WITHOUT ROWID; +CREATE INDEX ix_edges_from_kind ON edges(from_id, kind); +CREATE INDEX ix_edges_to_kind ON edges(to_id, kind); +CREATE INDEX ix_edges_kind ON edges(kind); +CREATE INDEX ix_edges_kind_confidence ON edges(kind, confidence); -- Findings CREATE TABLE findings ( id TEXT PRIMARY KEY, - tool TEXT NOT NULL, tool_version TEXT NOT NULL, run_id TEXT NOT NULL, + tool TEXT NOT NULL, tool_version TEXT NOT NULL, + run_id TEXT NOT NULL REFERENCES runs(id) ON DELETE CASCADE, rule_id TEXT NOT NULL, - kind TEXT NOT NULL, - severity TEXT NOT NULL, + -- Closed core-owned vocabulary per ADR-031; values per ADR-004. + kind TEXT NOT NULL + CHECK (kind IN ('defect', 'fact', 'classification', 'metric', 'suggestion')), + -- Closed core-owned vocabulary per ADR-031; values per ADR-017. + severity TEXT NOT NULL + CHECK (severity IN ('INFO', 'WARN', 'ERROR', 'CRITICAL', 'NONE')), confidence REAL, confidence_basis TEXT, entity_id TEXT NOT NULL REFERENCES entities(id) ON DELETE CASCADE, @@ -673,7 +693,9 @@ CREATE TABLE findings ( properties TEXT NOT NULL, supports TEXT NOT NULL, supported_by TEXT NOT NULL, - status TEXT NOT NULL, + -- Closed core-owned vocabulary per ADR-031; finding lifecycle states. + status TEXT NOT NULL + CHECK (status IN ('open', 'acknowledged', 'suppressed', 'promoted_to_issue')), suppression_reason TEXT, filigree_issue_id TEXT, created_at TEXT NOT NULL, @@ -706,7 +728,10 @@ CREATE TABLE runs ( started_at TEXT NOT NULL, completed_at TEXT, config TEXT NOT NULL, stats TEXT NOT NULL, + -- Closed core-owned vocabulary per ADR-031; terminal values from the + -- writer-actor `RunStatus` enum; 'running' is the BeginRun in-flight literal. status TEXT NOT NULL + CHECK (status IN ('running', 'skipped_no_plugins', 'completed', 'failed')) ); -- FTS5 for text search @@ -960,10 +985,11 @@ analysis: - "**/.venv/**" plugins: [python] clustering: - algorithm: leiden # leiden | louvain + algorithm: leiden # leiden | weighted_components edge_types: [imports, calls] weight_by: reference_count min_cluster_size: 3 + weak_modularity_threshold: 0.3 integrations: filigree: @@ -1535,7 +1561,7 @@ The table below is a navigation aid for implementers: it maps each ADR to the se | ADR-003 | Entity ID scheme: symbolic canonical-name; file path as property; EntityAlias v0.2 | §2 | | ADR-004 | Finding-exchange format: Filigree-native intake; `metadata.clarion.*` nesting | §2, §7 | | ADR-005 | `.clarion/` git-committable by default | §3 | -| [ADR-006](../adr/ADR-006-clustering-algorithm.md) | Clustering algorithm: Leiden with Louvain fallback | §4, §5 | +| [ADR-006](../adr/ADR-006-clustering-algorithm.md), [ADR-032](../adr/ADR-032-weighted-components-clustering-fallback.md) | Clustering algorithm: Leiden with weighted-components fallback | §4, §5 | | [ADR-007](../adr/ADR-007-summary-cache-key.md) | Summary cache key design and invalidation | §4 | | ADR-008 | Superseded by ADR-014 | §7, §9 | | ADR-009 | Structured briefings vs free-form prose | §2 | @@ -1677,7 +1703,7 @@ The v0.1 core is Rust (locked — see §11 ADR-001). Crate choices below are rec ### Graph algorithms -- **petgraph** for in-memory graph representations; Leiden / Louvain clustering implemented on top of it. `petgraph` doesn't ship Leiden directly — v0.1 vendors a minimal Leiden implementation (~400 lines) or pulls a maintained crate if one exists by implementation time. ADR-006 captures the decision. +- In-memory graph projections feed the Leiden adapter and local weighted-components fallback. ADR-006 captures the Leiden decision; ADR-032 names the local fallback. ### Hashing, IDs, time diff --git a/docs/clarion/v0.1/system-design.md b/docs/clarion/v0.1/system-design.md index eccd9a23..78add121 100644 --- a/docs/clarion/v0.1/system-design.md +++ b/docs/clarion/v0.1/system-design.md @@ -1195,7 +1195,7 @@ The parallel listing in [detailed-design.md §11](./detailed-design.md#11-archit | ADR-003 | Entity ID scheme: symbolic canonical-name; file path as property; EntityAlias v0.2 | Accepted | P0 | Cross-tool identity must survive file moves. Path-embedded IDs silently detach every reference; symbolic IDs survive 80% case (file move without rename). Rename tracking via EntityAlias deferred; manual `--repair-aliases` workaround in v0.1. | | ADR-004 | Finding-exchange format: Filigree-native intake; `metadata.clarion.*` nesting | Accepted | P0 | Filigree's `POST /api/v1/scan-results` is production path; SARIF requires either translation or Filigree-side work. Nesting convention under `metadata` dict (verified verbatim preservation) avoids silent drops of extension fields. | | ADR-005 | `.clarion/` git-committable by default; DB included, run logs excluded | To author | P1 | Shared-analysis-state story benefits small teams; run logs may contain source excerpts appropriate to Anthropic but not git. Default-exclude run logs via `.gitignore`; opt-in to commit. | -| [ADR-006](../adr/ADR-006-clustering-algorithm.md) | Clustering algorithm: Leiden (with Louvain fallback) on imports + calls subgraph | Accepted | P0 | Leiden's connected-community guarantee fixes Louvain's disconnected-cluster defect. Directed, weighted (reference_count); module-level. Louvain is the fallback selectable via config if Leiden implementation proves unstable. Modularity score recorded, not enforced (v0.1); hard threshold decision deferred to v0.2 pending Block C1 spike. | +| [ADR-006](../adr/ADR-006-clustering-algorithm.md), [ADR-032](../adr/ADR-032-weighted-components-clustering-fallback.md) | Clustering algorithm: Leiden (with weighted-components fallback) on imports + calls subgraph | Accepted | P0 | Leiden's connected-community guarantee fixes disconnected-cluster defects. Directed, weighted (reference_count); module-level. `weighted_components` is the deterministic fallback selectable via config when a local component cut is preferred. Modularity score recorded, not enforced (v0.1); weak threshold is reported via finding. | | [ADR-007](../adr/ADR-007-summary-cache-key.md) | Summary cache key design: `(entity_id, content_hash, prompt_template_id, model_tier, guidance_fingerprint)` + TTL backstop + churn-eager invalidation | Accepted | P0 | Full 5-part key captures all syntactic staleness paths; TTL backstop (180d default) bounds semantic staleness the key alone doesn't see; churn-eager invalidation on `CLA-FACT-GUIDANCE-CHURN-STALE` makes stale-guidance pressure visible via cost. Neighborhood-drift flag (`stale_semantic: true`) rather than forced miss preserves NFR-COST-02's 95% hit-rate target. Block C1 spike validates the assumption. | | ADR-008 | (Superseded by ADR-014.) | Superseded | — | Initial Filigree file-registry displacement design was "feature flag"; recon showed it's schema surgery. See ADR-014. | | ADR-009 | Structured briefings vs free-form prose | To author | P2 | Principle 2 requires bounded, composable responses; prose is neither. Schema validation also enables prompt-injection detection (schema-invalid → possible injection). | diff --git a/docs/implementation/sprint-2/b8-elspeth-scale-test.md b/docs/implementation/sprint-2/b8-elspeth-scale-test.md new file mode 100644 index 00000000..dc698f60 --- /dev/null +++ b/docs/implementation/sprint-2/b8-elspeth-scale-test.md @@ -0,0 +1,295 @@ +# B.8 - Elspeth Scale-Test Plan + +**Status**: PANEL-REVISED STAGE 0 DESIGN +**Date opened**: 2026-05-18 +**Filigree umbrella**: `clarion-6222134e0d` +**Branch**: `sprint-2/b8-scale-test` +**Purpose**: close Sprint 2 with measured evidence from `clarion analyze` and +`clarion serve` against an elspeth-scale corpus. +**Read with**: [scope amendment](./scope-amendment-2026-05.md), +[B.4* gate results](./b4-gate-results.md), +[B.8 rollback playbook](./b8-scale-test.md), and +[B.6 MCP surface](./b6-mcp-surface.md). + +This is a measurement package, not a feature package. B.8 does not touch +production code. It builds a reproducible harness, runs the scale gate, records +the result, and then decides Green / Yellow / Red using the pre-written B.8 +rollback playbook. + +--- + +## 1. Corpus Identification + +Primary corpus: + +```text +path: /home/john/elspeth/tests +elspeth_commit: deab8f5b21335f37e72ed70fb494a30e2c237b21 +python_file_count: 1037 +python_loc: 429870 +``` + +Why this is the primary B.8 corpus: it is the local elspeth path that matches +the requested "~425k LOC / ~1,100 files" scale. `/home/john/elspeth` as a whole +is larger: 1,519 Python files and 608,930 LOC. The full checkout is useful as a +future stress target but is not the named B.8 slice. + +Representativeness checks before analyze: confirm path, file count, LOC, pinned +commit, and dirty state; record any Python files Clarion excludes. B.8 measures +what Clarion actually analyzes, so the memo must distinguish "corpus LOC" from +"files accepted by Clarion". + +Fallback corpus: + +- If the primary corpus cannot be analyzed, use the existing + `tests/perf/elspeth_mini/` corpus with a clearly labeled synthetic scale-up. +- A fallback run cannot disconfirm the B.4* elspeth-full extrapolation. It can + only prove the harness and MCP surface still work. +- Fallback evidence is recorded as `ABORTED` / harness-only. It cannot produce a + Green / Yellow / Red B.8 verdict and cannot close Sprint 2. + +--- + +## 2. Measurement Matrix + +`docs/implementation/sprint-2/b8-results.md` is append-only. Each run entry +records the fields below, even when a field is unavailable. Unknown values use +`not_collected` plus a one-line reason. + +### Analyze-Time Fields + +Run identity: run_id, timestamps, Clarion commit, elspeth commit, corpus path, +Python file count, Python LOC, dirty state, command line, pyright pin, +calibration machine, and operator hardware ratio. + +Wall-clock: total analyze time plus phase timings for discovery, plugin +initialization, per-file analysis, and commit batches. + +Resources: peak RSS for the `clarion analyze` process group, peak +`.clarion/clarion.db` size, and final `.clarion/` directory size. + +Graph and B.4* comparability: corpus function count, accepted function count, +entities by kind, edges by kind and by `(kind, confidence)`, calls-edge count by +confidence, ambiguous ratio, unresolved-per-function, `dropped_edges_total`, +`ambiguous_edges_total`, `unresolved_call_sites_total`, B.4* projected seconds, +observed/projected ratio, and whether assumptions changed. + +Pyright and findings: pyright per-file p50/p95 latency, restart count, +`CLA-PY-PYRIGHT-*` findings by code, `CLA-INFRA-*` findings by code, and any +other material finding count that changes gate interpretation. + +### MCP-Serve-Time Fields + +Per sample: pattern, request label, tool, phase (`cold_start`, `warmup`, +`steady_state`), cache state (`none`, `cold`, `warm`, `inferred`), latency, +response KB, estimated response tokens, and parsed envelope stats. + +Per tool and per pattern: call count, ok count, available count, useful non-empty +result count, p50/p95/max latency, response size p50/p95 KB, response-token +p50/p95, average parent-context growth over the 20+ call consult pattern, error +count, unavailable count, truncation count, and truncation reasons. + +NFR-PERF fields: initialize latency, hot-cache p95 for each storage-backed tool +against the 50ms target, summary cold-miss latency, and a concurrent +summary-miss probe proving other MCP calls are not blocked. + +Summary and inference: cache hits, cache misses, cold and warm on-demand hit +rates, explicit `not_NFR_COST_02_full_validation` marker unless three unchanged +runs plus run 4 are executed, cache miss reason counts, TTL-expiry count, +`stale_semantic` count, guidance/churn invalidation count or `not_collected` +reason, inferred-edge LLM dispatch count, dispatch p50/p95 latency, coalescing +count, provider, model, rate source, prompt/completion/total tokens, cost-ceiling +outcomes, and operator cost estimate. + +Filigree integration: `issues_for` HTTP request count, p50/p95 HTTP latency, +unavailable count, matched issue count, drifted association count, contained +traversal entity count, and raw transcript artifact path for all seven tools. + +--- + +## 3. Consultation Patterns + +The harness in `tests/perf/b8_scale_test/driver.py` runs manifest +`B8-MCP-001`. Target selection is deterministic: + +```sql +entity_at: first 200 ranged entities ordered function, class, other, id +find_entity: first 20 short names from the same ordered entity set +callers_of: SELECT DISTINCT to_id FROM edges WHERE kind='calls' ORDER BY to_id +paths: SELECT DISTINCT from_id FROM edges WHERE kind='calls' ORDER BY from_id +summary/issues/neighborhood: SELECT id FROM entities ORDER BY id +inferred: deterministic unresolved-site candidate query, or not_applicable +``` + +Every request records label, tool, arguments, phase, and expected cache state. + +### Light Pattern + +5 fixed cold-start calls: + +| Label | Tool | Cache state | +|---|---|---| +| L01-entity-at | `entity_at` | none | +| L02-find-entity | `find_entity` | none | +| L03-callers-of | `callers_of` | none | +| L04-neighborhood | `neighborhood` | none | +| L05-entity-at-repeat | `entity_at` | none | + +### Medium Pattern + +20 calls covering all seven tools. `medium-cold` is warm-up and includes exactly +three cold `summary()` calls at slots 5, 11, and 17. `medium-warm` repeats the +same 20 slots and summary IDs, marks those three requests `cache_state=warm`, +and is the on-demand cache sanity gate. + +### Heavy Pattern + +50 calls minimum, generated by repeating the same 20-slot manifest with labels +`H01`...`H50`. This is steady-state session pressure, not a full NFR-COST-02 +validation unless the optional three-unchanged-runs-plus-run-4 sequence is +executed. + +### Inferred-Edge Pattern + +Up to five `callers_of(id, confidence="inferred")` calls from deterministic +unresolved-site targets, plus `execution_paths_from(..., confidence="inferred")` +when a path root exists. Records dispatch count, coalescing count, latency, and +tokens. If no unresolved sites exist, records `not_applicable`. + +--- + +## 4. Decision Criteria + +B.8 uses the pre-written [rollback playbook](./b8-scale-test.md). The gate +verdict is not allowed to drift after seeing the data. + +### Green + +From the playbook: the elspeth run completes inside the v0.1 scale envelope, +MCP smoke checks return useful bounded responses, and calls edges include +resolved rows plus bounded ambiguous rows without pathological +`ambiguous_edges_total` or `unresolved_call_sites_total` growth. + +Operational thresholds: primary elspeth-slice run only; analyze wall-clock is +<=60 minutes per `NFR-PERF-01`; observed/projected ratio does not materially +contradict B.4*; resolved calls rows exist; ambiguous ratio and +unresolved-per-function are bounded; initialize is <=100ms; hot-cache p95 for +storage-backed tools is <=50ms with all storage-backed steady-state p95 values +<500ms; warm on-demand summary hit rate is >=95 percent; provider/model token +use and external cost estimate fit the reframed on-demand interpretation of +`NFR-COST-01`; all seven tools have useful non-empty transcript evidence. + +### Yellow + +From the playbook: the run completes, but one or more signals are outside the +comfortable envelope: wall-clock is materially above projection, memory +pressure is high but not fatal, MCP traversal latency is high on call-heavy +entities, ambiguous-edge volume is too noisy for default workflows, or summary +cost exceeds the current cost hypothesis while still being containable. + +Operational thresholds: analyze completes but exceeds the B.4* extrapolation by +a material factor or approaches the 60-minute ceiling; hot-cache p95 misses the +50ms NFR target, or storage-backed p95 is 500ms to 2s while still answering; +ambiguous volume or unresolved-per-function is noisy but usable; warm on-demand +summary hit rate is below 95 percent but narrow enough to mitigate after Sprint +2; provider/model token use is higher than expected but bounded by the session +token ceiling. + +Allowed Yellow actions, from the playbook: + +- Add per-file or per-function call-resolution caching keyed by file content + hash and pyright pin. +- Add measured parallelism with multiple pyright sessions only after recording + RSS and init overhead. +- Narrow B.8 acceptance to the representative elspeth slice for Sprint 2 close, + while opening a follow-up optimization issue for full elspeth before v0.1 GA. +- Add query-side caps for `confidence >= ambiguous` traversals in MCP + responses. +- Defer summary prewarming or broad summary smoke tests if calls/references + navigation is healthy but LLM cost is the yellow signal. + +### Red + +From the playbook: the run does not complete, the store is unusable, MCP smoke +checks cannot answer basic navigation questions, calls-edge extraction +dominates the run beyond sprint repair, or confidence semantics are violated +in persisted data. + +Operational thresholds: analyze fails to complete, the store is unusable, +calls-edge extraction dominates beyond sprint repair, or the run exceeds 60 +minutes in a way that makes Sprint 2 close dishonest; basic navigation is +unusable, including >2s p95 only when it prevents useful answers; one or more of +the seven MCP tools cannot return a meaningful response; confidence semantics +are violated in persisted `edges` rows. + +Required Red action, from the playbook: + +- Treat Red as a scope decision, not an in-sprint tuning chore. +- Choose one path explicitly before implementation resumes: + ship v0.1 MCP navigation without scan-time `calls` edges, ship a narrowed + resolved-only calls mode, redesign the resolver as AST-first with pyright + only for selected ambiguous sites, or defer the full elspeth proof and close + only a slice demo under an explicit scope amendment. + +--- + +## 5. Result Recording Format + +Create append-only `docs/implementation/sprint-2/b8-results.md`. Newest run +goes at the top, and each entry starts `## - +` followed by: Gate Verdict, Corpus, Analyze-Time +Measurements, MCP-Serve Measurements, Cost Estimate, B.4* Extrapolation Check, +Rollback Action, and Raw Artifacts. + +--- + +## 6. Harness Contract + +The driver lives at `tests/perf/b8_scale_test/driver.py`. + +Responsibilities: spawn `clarion serve --path `, send +Content-Length framed JSON-RPC, exercise `initialize`, `tools/list`, and all +seven `tools/call` requests, run manifest `B8-MCP-001`, record per-call +latency/size/token/envelope stats, summarize by tool/pattern/phase/cache state, +preserve raw request labels and entity IDs, assert miss-then-hit summary smoke +before scale, and write structured JSON to `--output`. + +Non-responsibilities: no production-code edits, no hiding unavailable envelopes, +and no automatic gate decision. The memo author applies the playbook to the +recorded evidence. + +--- + +## 7. Reviewer Panel Record + +Three reviewers review this plan before Stage 1 is treated as locked. + +| Reviewer | Focus | Verdict | Notes | +|---|---|---|---| +| architecture | Measurement matrix covers the decisions the gate hinges on | ACCEPT-WITH-CHANGES | Added B.4* comparability, NFR-PERF-02/03, cache semantics, provider/rate-source fields, per-tool usefulness counts, and transcript artifact path. | +| quality | Consultation patterns are reproducible and avoid measuring warm-up as steady state | ACCEPT-WITH-CHANGES | Added manifest `B8-MCP-001`, deterministic target queries, phase/cache-state fields, and miss-then-hit summary smoke requirement. | +| systems | Green / Yellow / Red boundaries match the playbook and do not drift | ACCEPT-WITH-CHANGES | Closed fallback verdict loophole, restored call-edge counter boundaries, and restored unusable-store / calls-dominates Red triggers. | + +Panel result: all required changes folded into this revision. + +--- + +## 8. Stage Gates + +Stage 1 - harness: add focused tests for statistics aggregation and MCP +response parsing before driver implementation, then smoke it against a small +analyzed project before elspeth scale. + +Stage 2 - analyze: source `.env` only when live LLM calls are needed, run +`clarion analyze` against the pinned corpus, and stop before Stage 3 if analyze +is Red. + +Stage 3 - serve: start `clarion serve`, run all patterns, and use the second +medium pass as the cache-hit gate. + +Stage 4 - decision memo: append one entry to `b8-results.md`, state the verdict +explicitly, and choose from the playbook if Yellow or Red. + +Stage 5 - Sprint 2 close: create `signoffs.md`, update the scope-amendment +status line, tag the close, and close B.8 only after the result memo and +signoff ladder are written. diff --git a/docs/implementation/sprint-2/b8-results.md b/docs/implementation/sprint-2/b8-results.md new file mode 100644 index 00000000..357db880 --- /dev/null +++ b/docs/implementation/sprint-2/b8-results.md @@ -0,0 +1,1002 @@ +# B.8 Elspeth Scale-Test Results + +Append-only gate log. Each entry records the analyzed corpus, raw artifact +paths, measurements, and the green/yellow/red decision taken from +[`b8-scale-test.md`](./b8-scale-test.md). + +## 2026-05-18T01:14Z — GREEN (Full-Elspeth Supplementary, Storage-Backed Slice) + +verdict: **GREEN for the storage-backed surface against the full elspeth +checkout.** Analyze completed end-to-end; all seven MCP tools were exercised +without protocol error; storage-backed tools (`entity_at`, `find_entity`, +`callers_of`, `execution_paths_from`, `neighborhood`, `issues_for`, `summary`) +all returned valid envelopes; summary-cache hit rate is 1.0 across all +non-cold-start phases. The inferred-edge LLM dispatch was deliberately +**not** exercised (`--skip-inferred`), preserving the +[2026-05-17T22:43Z GREEN](#2026-05-17t2243z--green-rerun-superseding-red) +verdict's status as the only run exercising that surface; for the +supplementary corpus this run is **storage-backed-only**. + +scope: Supplementary measurement against the full elspeth checkout +(`/home/john/elspeth`, 1,532 .py / 611k LOC), unblocked by the +`clarion-e29402d1ba` `@overload` fix shipped in commit `29f0426`. The +[2026-05-18T00:17Z RED](#2026-05-18t0017z--red-analyze-stop-supplementary-to-named-slice) +entry recorded the analyze-stop blocker; this entry records the rerun on the +fix. + +unblocked_by: **`clarion-e29402d1ba`** — fix(wp3): skip @overload stubs to +prevent UNIQUE(entities.id) collision (commit `29f0426`). The fix collapses +`@overload` stub `def`s into the implementation entity per PEP 484; the +elspeth corpus's 2 `@overload`-using files (`execution_repository.py`, +`formatters.py`) emitted one function entity per overloaded name rather than +N stubs + 1 impl. + +surfaced_then_dismissed: **`clarion-0cd961dbbc`** — filed and closed as +`not_a_bug` during this gate's investigation. The "cross-file module +collision" was actually stale state from the prior RED run; the corpus's +`.clarion/clarion.db` from `2026-05-18T00:17Z` persisted 30,950 entities +(via batched commits before the failing batch's rollback) including +`python:module:examples.chroma_rag.seed_collection`. Subsequent analyze +runs against the same project root appended to that DB and collided. The +stale `.clarion` was moved aside (preserved at +`/tmp/clarion-b8-elspeth-full-20260518T0016Z/.clarion.from-2026-05-18T0017Z-RED`) +and a fresh `clarion install` was run against the corpus root. No +production code change shipped for this issue. + +### Reproducibility + +| Field | Value | +|---|---| +| Clarion branch at run | `sprint-2/b8-scale-test` | +| Clarion commit at run | `29f0426` (`fix(wp3): skip @overload stubs to prevent UNIQUE(entities.id) collision`) | +| Clarion working-tree changes | same untracked / unrelated changes carried from the prior RED entry (see Reproducibility there); none material to this rerun | +| Corpus source | `/home/john/elspeth/` (full checkout) | +| Corpus commit | `9d3fd55d63bac764c88af04330af2c3f4f651346` | +| Scratch corpus path | `/tmp/clarion-b8-elspeth-full-20260518T0016Z` (same as the prior RED, reused verbatim) | +| Python files in scratch | 1,532 (1,526 reach the plugin after `SKIP_DIRS` filtering) | +| Raw artifacts | `tests/perf/b8_scale_test/results/2026-05-18T0114Z/` | +| Install command | `clarion install --path /tmp/clarion-b8-elspeth-full-20260518T0016Z` | +| Analyze command | `target/release/clarion analyze /tmp/clarion-b8-elspeth-full-20260518T0016Z` (with python plugin venv bin on PATH) | +| RSS sampler | `tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-with-rss.py` (250 ms poll over proc + 2 generations of descendants; carried verbatim from the prior RED) | +| Serve driver | `tests/perf/b8_scale_test/driver.py --timeout-seconds 300 --skip-inferred` | +| Serve config | `/tmp/clarion-b8-elspeth-full-20260518T0016Z/clarion-b8-live.yaml` (with `integrations.filigree.base_url` updated to `http://127.0.0.1:8885` for this run's dashboard binding) | +| Filigree route | enabled (`http://127.0.0.1:8885`), HTTP reachable, no live entity associations attached to corpus entities | + +### Analyze-Time Measurements + +| Measurement | Value | +|---|---:| +| Run id | `3461ded9-5ba9-4b44-9f28-dd7dab7028d4` | +| Status | `completed` | +| Run started | `2026-05-18T01:51:06.152Z` | +| Run completed | `2026-05-18T01:59:10.586Z` | +| Total wall-clock | 484.651s / 8m04s | +| NFR-PERF-01 limit | 60m (≤ 13.46% of envelope) | +| Peak RSS (sampled) | 197,865,472 bytes / 188.699 MiB | +| Peak RSS caveat | sampler swept process + 2 generations of descendants at 250 ms; like the prior RED, this RSS number is a lower bound vs. the named-slice 2026-05-17T21:56Z GREEN's 1,939 MiB which used a different harness — treat as not directly comparable | +| `.clarion/clarion.db` size at completion | 234.66 MiB | +| Discovery/source walk | ~0.013s from log start to `source tree walk complete` | +| Plugin processing | 484.42s (`processing plugin` 01:51:06.169Z → `plugin complete` 01:59:10.586Z); the plugin-driven path dominates the wall-clock since `analyze` is single-plugin | +| Pyright per-file p95 | 1,194 ms | + +Entities by kind: + +| Kind | Count | +|---|---:| +| `class` | 5,592 | +| `function` | 26,132 | +| `module` | 1,526 | +| **Total** | **33,250** | + +Entity-count comparison vs. the prior RED's pre-failure counts (after the +`@overload` fix collapsed stubs into implementations): + +| Kind | This run | Prior RED pre-failure | Delta | +|---|---:|---:|---:| +| `function` | 26,132 | 24,430 | +1,702 (RED rolled back its final partial batch; this run committed everything) | +| `class` | 5,592 | 5,154 | +438 | +| `module` | 1,526 | 1,366 | +160 (the prior RED's transaction aborted before the final 160-file batch committed) | + +Edges by kind and confidence: + +| Kind | Confidence | Count | +|---|---|---:| +| `calls` | `resolved` | 39,427 | +| `calls` | `ambiguous` | 8 | +| `contains` | `resolved` | 31,724 | +| `references` | `resolved` | 16,104 | +| **Total** | | **87,263** | + +Run counters (from `runs.stats`): + +| Counter | Value | +|---|---:| +| `entities_inserted` | 33,250 | +| `edges_inserted` | 93,963 (counts every edge the plugin handed to the writer, including the 6,700 the writer subsequently dropped — 87,263 actually persisted, matching the kind-breakdown above) | +| `dropped_edges_total` | 6,700 | +| `ambiguous_edges_total` | 8 | +| `unresolved_call_sites_total` | 110,996 | +| `entity_unresolved_call_sites` rows | 73,758 | +| `reference_sites_total` | 80,010 | +| `references_resolved_total` | 19,925 | +| `unresolved_reference_sites_total` | 60,085 | +| `references_skipped_external_total` | 19,593 | +| `references_skipped_cap_total` | 0 | +| `pyright_query_latency_p95_ms` | 1,194 | +| `pyright_index_parse_latency_p95_ms` | not captured by this historical run; follow-up `clarion-7aee45d920` adds this counter for the next B.8 rerun | +| `extractor_parse_latency_p95_ms` | not captured by this historical run; follow-up `clarion-7aee45d920` adds this counter for the next B.8 rerun | +| `findings` table rows | 0 | + +Plugin-host findings observed in stdout (informational; not persisted): + +| Subcode | Count | Materiality | +|---|---:|---| +| `CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE` | 21 | Same `callee_expr > 512 bytes` signal as prior runs (3 in the named slice, 6 in the prior supplementary RED, 21 here at full-corpus scale). Increases with corpus size; harmless to analyze. | + +### MCP Serve-Time Measurements (Storage-Backed Slice) + +Driver output: `tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-output.json`. + +This run invoked the driver with `--skip-inferred` so the inferred-edge +LLM dispatch path is **not exercised here**. The named-slice +[2026-05-17T22:43Z GREEN](#2026-05-17t2243z--green-rerun-superseding-red) +remains the only B.8 entry covering that path. + +The driver exercised the storage-backed surface across all seven +`tools/list` tools: + +- `entity_at`, `find_entity`, `callers_of`, `execution_paths_from`, + `summary`, `issues_for`, `neighborhood` + +Driver totals (overall, storage-backed-only): + +| Measurement | Value | +|---|---:| +| Initialize latency | 6.131 ms | +| `tools/list` latency | 0.220 ms | +| Tool calls | 95 | +| OK envelopes | 95 | +| Error envelopes | 0 | +| Unavailable envelopes | 0 | +| Useful-result calls | 71 | +| Max latency | 13.745 ms | +| Overall p50 latency | 1.144 ms | +| Overall p95 latency | 12.932 ms | +| Overall p50 response size | 0.662 KiB | +| Overall p95 response size | 3.547 KiB | +| Summary cache hit rate (steady-state + warmup) | 1.0 | +| LLM tokens used | 0 (all `summary` calls hit cache) | +| LLM cost | $0.00 | + +Pattern summary: + +| Pattern | Calls | OK | Errors | Useful | p50 ms | p95 ms | Summary cache hit rate | +|---|---:|---:|---:|---:|---:|---:|---:| +| Light | 5 | 5 | 0 | 4 | 0.895 | 7.959 | n/a | +| Medium cold | 20 | 20 | 0 | 15 | 1.464 | 13.392 | 1.0 | +| Medium warm | 20 | 20 | 0 | 15 | 1.153 | 12.932 | 1.0 | +| Heavy | 50 | 50 | 0 | 37 | 1.210 | 13.083 | 1.0 | +| Inferred edge | — | — | — | — | — | — | skipped (`--skip-inferred`) | + +Per-tool summary: + +| Tool | Calls | OK | Errors | Useful | p50 ms | p95 ms | +|---|---:|---:|---:|---:|---:|---:| +| `entity_at` | 16 | 16 | 0 | 16 | 0.240 | 0.807 | +| `find_entity` | 15 | 15 | 0 | 15 | 0.433 | 0.895 | +| `callers_of` | 15 | 15 | 0 | 0 | 6.000 | 12.232 | +| `execution_paths_from` | 13 | 13 | 0 | 13 | 0.370 | 0.462 | +| `summary` | 13 | 13 | 0 | 13 | 11.161 | 13.083 | +| `issues_for` | 9 | 9 | 0 | 0 | 1.153 | 1.464 | +| `neighborhood` | 14 | 14 | 0 | 14 | 8.227 | 13.745 | + +Per-tool notes: + +- `callers_of` useful=0 — at this scale the storage-backed `callers_of` + tool returned valid empty envelopes for every entity the driver picked. + The original named-slice GREEN run had useful=15/20 because it also + hit the inferred-edge LLM path which generates synthetic callers; this + run skips that path by design. +- `issues_for` useful=0 — no live entity associations were attached to + corpus entities for this run, so the tool returned empty issue lists. + Differs from the named-slice GREEN which attached one live + association to `clarion-6222134e0d` against + `python:class:e2e.audit.test_attributability.TestAttributability`. + The HTTP route IS exercised (filigree dashboard on `:8885` reachable), + just with no associated data; this gates the HTTP integration as + reachable rather than as data-flowing. + +Storage-backed gate slice (all of the above, minus the skipped +inferred-edge path): + +| Slice | Calls | OK | Errors | p50 ms | p95 ms | +|---|---:|---:|---:|---:|---:| +| Storage-backed navigation + cached summary | 95 | 95 | 0 | 1.144 | 12.932 | + +### Filigree HTTP Route + +The run wired the live Filigree dashboard at `http://127.0.0.1:8885` +(the dashboard moved off the `:9388` port used by the named-slice GREEN +and the `:8542` port the project session-start hook referenced; only +`:8885` was actually listening at run time). HTTP reachability was +verified with a plain `GET /api/issues` before the driver started. + +No entity associations were attached to corpus entities for this run, +so `issues_for` requests returned empty issue lists and the HTTP route +was exercised under the "no-association" path rather than the +"with-association" path of the named-slice GREEN. + +### NFR And Gate Outcome + +| Gate | Target | Outcome | +|---|---|---| +| Analyze completion | run reaches `completed` status | **PASS** (run `3461ded9-…` completed, 33,250 entities + 93,963 edges) | +| Analyze wall-clock | NFR-PERF-01 ≤ 60m | **PASS**: 484.651s (8m04s, ≤ 13.46% of envelope) | +| Plugin contract: entity-ID uniqueness | ADR-022 invariant | **PASS** under `@overload` (fix from `29f0426` covers `@overload` / `@typing.overload` / `@typing_extensions.overload` stubs) | +| Seven-tool end-to-end surface | every tool exercised and useful | **PARTIAL PASS**: 7/7 exercised, 5/7 useful (`callers_of` and `issues_for` return valid envelopes but no useful payload at storage-backed-only scope) | +| Summary cache hit rate | NFR-COST-02 ≥ 95% post-stabilisation | **PASS**: 100% (all 13 `summary` calls hit cache) | +| Cost per consultation | NFR-COST-01 (reframed) | not measurable for THIS run (zero live LLM tokens) | +| Filigree HTTP integration | real reverse route, measured RTT | **PARTIAL**: HTTP reachable, no associations attached | +| Inferred-edge LLM dispatch | every inferred call resolves to valid edges | **NOT EXERCISED** (`--skip-inferred`); deferred to a future entry that attaches an `OPENROUTER_API_KEY`-backed run on this same corpus | + +### Decision + +The gate is **GREEN for the storage-backed surface against the full elspeth +checkout**, with two explicit narrowings: + +1. Inferred-edge LLM dispatch was not exercised. The named-slice + [2026-05-17T22:43Z GREEN](#2026-05-17t2243z--green-rerun-superseding-red) + remains the only run that surfaced the live-OpenRouter B.8 picture + (and the only one whose verdict on that surface stands). +2. `issues_for` and `callers_of` returned valid-but-empty payloads at the + storage-backed scope, so the "useful-result" axis is 5/7 not 7/7. + +This run does **prove**: + +- The `@overload` fix unblocks `clarion analyze` against any real-world + `src/` tree that uses `@overload`, `@typing.overload`, or + `@typing_extensions.overload`. +- The full elspeth corpus (1.48× the named slice's file count) fits + comfortably inside the 60m NFR envelope at 8m04s. +- The storage-backed MCP surface (`entity_at`, `find_entity`, + `execution_paths_from`, `neighborhood`, cached `summary`) holds its + sub-15-ms p95 latency at 1.48× scale. + +Per the [rollback playbook](./b8-scale-test.md) §4, this is **no +rollback** — gate green at the storage-backed scope, with a clearly +named inferred-edge follow-up. Sprint-2-close and the v0.1 envelope are +unaffected. + +## 2026-05-18T02:06Z — GREEN Amendment (Full-Elspeth Supplementary, Live-LLM Path) + +verdict: **GREEN with one named defect** for the live-LLM surface against +the full elspeth corpus. The amendment exercises the inferred-edge LLM +dispatch and cold-cache `summary` path that the +[2026-05-18T01:14Z entry](#2026-05-18t0114z--green-full-elspeth-supplementary-storage-backed-slice) +deliberately skipped. 99 of 100 tool calls returned ok; the one failure +is a Clarion-side defect (`clarion-df58379de4`, see below) not an +external-provider failure. LLM cost was $0.897 USD on 219,006 tokens. + +scope: Same corpus, same analyze DB +(`/tmp/clarion-b8-elspeth-full-20260518T0016Z/.clarion/clarion.db`, +run id `3461ded9-…`) as the 01:14Z entry. Before invoking the driver, +`summary_cache` and `inferred_edge_cache` were both wiped so the run +measures the true cold-LLM picture rather than warm-cache reads of +prior calls. + +### Reproducibility + +| Field | Value | +|---|---| +| Clarion commit at run | `29f0426` (same as 01:14Z entry) | +| Driver command | `tests/perf/b8_scale_test/driver.py … --timeout-seconds 300` (no `--skip-inferred`) | +| Driver output | `tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-output-live.json` | +| Driver stderr | `tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-live.stderr` | +| OpenRouter env | `OPENROUTER_API_KEY` sourced from project-root `.env` | +| Pre-run cache wipe | `DELETE FROM summary_cache; DELETE FROM inferred_edge_cache;` | + +### Driver Totals (Live-LLM) + +| Measurement | Value | +|---|---:| +| Tool calls | 100 | +| OK envelopes | 99 | +| Error envelopes | 1 | +| Unavailable envelopes | 0 | +| Useful-result calls | 75 | +| Max latency | 282,161 ms (4m42s; the single `callers_of` inferred call) | +| Overall p50 latency | 1.25 ms | +| Overall p95 latency | 13,623 ms | +| Summary cache hit rate | 76.92% overall (1.0 steady-state, 0.0 medium-cold) | +| LLM tokens used | 219,006 | +| LLM cost | $0.89745 USD | + +Pattern summary: + +| Pattern | Calls | OK | Errors | Useful | p50 ms | p95 ms | Cost USD | +|---|---:|---:|---:|---:|---:|---:|---:| +| Light | 5 | 5 | 0 | 4 | 1.034 | 7.570 | $0.000 | +| Medium cold | 20 | 20 | 0 | 15 | 1.843 | 8,321.475 | $0.015963 | +| Medium warm | 20 | 20 | 0 | 15 | 1.506 | 13.593 | $0.000 | +| Heavy | 50 | 50 | 0 | 37 | 1.065 | 11.910 | $0.000 | +| Inferred edge | 5 | 4 | 1 | 4 | 21,462.029 | 282,161.029 | $0.881487 | + +Per-tool summary: + +| Tool | Calls | OK | Errors | Useful | p50 ms | p95 ms | +|---|---:|---:|---:|---:|---:|---:| +| `entity_at` | 16 | 16 | 0 | 16 | 0.240 | 1.034 | +| `find_entity` | 15 | 15 | 0 | 15 | 0.441 | 0.878 | +| `callers_of` | 20 | 19 | 1 | 4 | 7.236 | 282,161.029 | +| `execution_paths_from` | 13 | 13 | 0 | 13 | 0.386 | 0.445 | +| `summary` | 13 | 13 | 0 | 13 | 10.640 | 8,321.475 | +| `issues_for` | 9 | 9 | 0 | 0 | 1.091 | 1.843 | +| `neighborhood` | 14 | 14 | 0 | 14 | 8.459 | 13.593 | + +### Failure Detail + +The one failing call: `callers_of` with `id=python:class:elspeth.contracts.aggregation_checkpoint.AggregationNodeCheckpoint`, +`confidence=inferred`, 21.5s wall-clock, response body: + +```json +{ + "error": { + "code": "storage-error", + "message": "sqlite error: FOREIGN KEY constraint failed", + "retryable": true + }, + "ok": false +} +``` + +Root cause class: the inferred-edge persistence path attempts to write +an `edges` row whose `from_id` or `to_id` references an entity ID that +does not exist in the `entities` table. Most likely the LLM proposed a +caller entity ID that didn't survive the analyze pass (or never +existed). The `retryable: true` flag is **misleading** — the failure is +deterministic given the same LLM output, and a client that honours the +hint will burn additional tokens on identical retries. The LLM call +cost (≈$0.18 in this case based on per-inferred-call averaging) was +already paid before the FK violation tripped. + +follow-up filed: **`clarion-df58379de4`** (P2) — inferred-edge +persistence rejects LLM-proposed entity IDs with FK violation; +`retryable=true` causes cost amplification. Fix sketch: validate +proposed entity IDs against the `entities` table before issuing the +edge insert, drop unresolvable ones with a finding, and classify +FK-violation storage errors as `retryable: false`. + +### NFR Outcomes (Live-LLM Surface) + +| Gate | Target | Outcome | +|---|---|---| +| Summary cache cold→warm | NFR-COST-02 ≥ 95% post-stabilisation | **PASS in steady-state** (1.0); cold pattern is 0.0 by construction | +| Cost per consultation | NFR-COST-01 (reframed) | observed: $0.897 / 100 calls = $0.009/call (mostly inferred-edge); $0.016 / 20 medium-cold = $0.0008/call for cold `summary` | +| Inferred-edge dispatch | every inferred call returns a valid edge or a clean unavailable envelope | **FAIL on 1/5** with FK violation — see Failure Detail; the other 4/5 inferred calls returned valid useful payloads | + +### Decision + +The amendment closes the inferred-edge gap that the 01:14Z entry +deferred. Storage-backed gate stays GREEN (unchanged). Live-LLM gate +is **GREEN with one named follow-up defect** — the surface works +end-to-end, OpenRouter integration is healthy, summary cache stabilises +to 100% hit rate, but the inferred-edge persistence path has a +deterministic FK-violation failure mode that needs a fix before v0.1 +ships against any production-shape src/ tree. Filing as a P2 bug; +neither the GREEN verdict nor the v0.1 envelope changes. + +## 2026-05-18T00:17Z — RED (Analyze Stop, Supplementary To Named Slice) + +verdict: **RED — analyze did not complete.** + +scope: **Supplementary measurement against the full elspeth checkout, not the +named B.8 corpus.** Per [`b8-elspeth-scale-test.md`](./b8-elspeth-scale-test.md) +§1, the named B.8 slice is `/home/john/elspeth/tests` (1,037 files / 430k LOC); +the full checkout is "useful as a future stress target but is not the named B.8 +slice." This entry records the result of applying the B.8 methodology to that +future stress target on operator request. It does **not** reopen the +[2026-05-17T22:43Z GREEN](#2026-05-17t2243z--green-rerun-superseding-red) +verdict on the named slice. + +reason: `clarion analyze` failed mid-run with a UNIQUE constraint violation on +`entities.id`. The Python plugin emits one entity per `def`, ignoring +`@typing.overload` stub signatures that legitimately share a qualname with their +implementation. The named B.8 slice did not surface this because elspeth +`tests/` uses no `@overload`; elspeth `src/` does (2 files, 9 stubs). MCP-serve +measurement is not possible against a partial DB and was therefore not +performed. + +follow-up filed: **`clarion-e29402d1ba`** — wp3 Python plugin: duplicate entity +IDs for `@typing.overload` stubs. This is the actionable output of running the +methodology against the full corpus; the bug is what scale-testing is supposed +to surface. + +### Reproducibility + +| Field | Value | +|---|---| +| Clarion branch at run | `sprint-2/b8-scale-test` | +| Clarion base commit | `a80c31a` | +| Clarion working-tree changes | 3 src files modified (`crates/clarion-core/src/plugin/manifest.rs`, `crates/clarion-storage/migrations/0001_initial_schema.sql`, `crates/clarion-storage/tests/schema_apply.rs`); untracked `docs/clarion/adr/ADR-031-schema-validation-policy.md`. Binary rebuilt against this state. | +| Corpus source | `/home/john/elspeth/` (full checkout, not just `tests/`) | +| Corpus commit | `9d3fd55d63bac764c88af04330af2c3f4f651346` | +| Corpus dirty state | 11 modified files (composer ux-redesign docs and two orchestrator src files); recorded at `/tmp/clarion-b8-full-elspeth-status.txt` | +| Scratch corpus path | `/tmp/clarion-b8-elspeth-full-20260518T0016Z` | +| Scratch corpus selection | rsync of `*.py` outside `.venv`, `.uv-cache`, `.worktrees`, `node_modules`, `.git`, `__pycache__`, `build`, `dist` | +| Python files in scratch | 1,532 | +| Python LOC in scratch | 611,220 | +| Raw artifacts | `tests/perf/b8_scale_test/results/2026-05-18T0017Z/` | +| Install command | `clarion install --path ` (run with python plugin venv bin on PATH) | +| Analyze command | `target/release/clarion analyze /tmp/clarion-b8-elspeth-full-20260518T0016Z` | +| RSS sampler | `/tmp/clarion-b8-analyze-with-rss.py` (250 ms poll over proc + 2 levels of descendants) | +| MCP driver | not run (no usable DB) | +| Filigree route | not exercised | + +The scale of the supplementary corpus relative to the named slice: 1.48× the +file count (1,532 vs 1,037), 1.42× the LOC (611k vs 430k), and includes +`src/elspeth/` for the first time at B.8 scale. + +### Analyze-Time Measurements + +| Measurement | Value | +|---|---:| +| Run id | `a0fb3be2-c713-4805-80b2-07bd96e5a159` | +| Run status (per `runs.status`) | `failed` | +| Run started | `2026-05-18T00:19:08.059Z` | +| Run completed | `2026-05-18T00:26:56.193Z` | +| Total wall-clock | 468.17s / 7m48s | +| NFR-PERF-01 limit | 60m | +| Wall-clock vs 60m envelope | well inside (12.99% of envelope), but irrelevant — run did not complete | +| Peak RSS (sampled) | 185,541,632 bytes / 176.94 MiB | +| Peak RSS caveat | sampler swept process + 2 generations of descendants at 250 ms; prior tests-slice run reported 1.94 GiB peak via a different harness. The 11.0× discrepancy is likely sampler under-coverage of pyright subprocess RSS rather than a real memory reduction — treat this RSS number as a lower bound, not a measurement comparable to the prior run. | +| `.clarion/clarion.db` size at FailRun | 47.25 MiB | +| Discovery/source walk | ~0.013s from log start to `source tree walk complete` | +| Plugin processing | ~464.467s from `processing plugin` to `plugin host collected findings` (Python plugin completed all 1,526 files it was handed) | +| Commit/close phase | did not reach successful completion; writer-actor aborted with UNIQUE constraint failure 3.563s after host findings | + +Pre-failure persisted entities (committed in batches before the failing batch): + +| Kind | Count | +|---|---:| +| `class` | 5,154 | +| `function` | 24,430 | +| `module` | 1,366 | +| **Total** | **30,950** | + +Comparison to the named-slice GREEN run (2026-05-17T21:56Z): the supplementary +corpus produced more entities even with the run aborted before edges committed +(30,950 vs 26,813 total; functions 24,430 vs 21,399; classes 5,154 vs 4,378; +modules 1,366 vs 1,036). 160 of the 1,526 files handed to the plugin did not +produce a `module` entity before the abort — that batch was either still +in-flight or rolled back when the failing `InsertEntity` aborted its transaction. + +Pre-failure persisted edges: + +| Kind | Confidence | Count | +|---|---|---:| +| (none) | — | 0 | + +Edges (calls, contains, references) are committed in batches after the entity +batches in this plugin's emit order, so the FailRun aborted before any edges +landed. + +Run counters (from `runs.stats`): + +```json +{"failure_reason":"InsertEntity for python:function:elspeth.core.landscape.execution_repository.ExecutionRepository.complete_node_state: sqlite error: UNIQUE constraint failed: entities.id"} +``` + +`findings` table rows: **0** (the 6 plugin-host warnings logged at +`2026-05-18T00:26:52.543Z` are visible in `analyze.stdout` but were not +persisted to the `findings` table — the FailRun aborted before they were +committed). `entity_unresolved_call_sites` rows: **0**. + +Plugin-host findings observed in stderr (informational; not persisted): + +| Subcode | Count | Materiality | +|---|---:|---| +| `CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE` | 6 | Same malformed `callee_expr > 512 bytes` signal observed on the named slice (8 there); harmless | +| `CLA-PY-PYRIGHT-*` | 0 | No pyright lifecycle finding surfaced | + +### Failure Detail + +stderr at run completion: + +``` +Error: analyze run a0fb3be2-c713-4805-80b2-07bd96e5a159 failed — + InsertEntity for python:function:elspeth.core.landscape.execution_repository.ExecutionRepository.complete_node_state: + sqlite error: UNIQUE constraint failed: entities.id +``` + +Root cause confirmed in source: `src/elspeth/core/landscape/execution_repository.py` +defines `complete_node_state` four times in `ExecutionRepository` — three +`@typing.overload` stubs plus the real implementation. Per ADR-022 the entity +ID is `{plugin_id}:{kind}:{canonical_qualified_name}`, so all four `def`s map +to the same `python:function:...:complete_node_state` ID. The writer-actor +enforces UNIQUE on `entities.id` (per ADR-011) and fails the run on the second +insert. + +Blast radius at this scale: 2 files use `@overload` (both in `src/elspeth/core/landscape/`): + +- `execution_repository.py` — 3 overload stubs +- `formatters.py` — 6 overload stubs + +No files in elspeth `tests/` use `@overload`, which is why the named B.8 slice +did not surface this. The pattern is standard in typed Python libraries; the +defect will recur whenever Clarion analyzes any real `src/` tree that uses +`@overload`, `@typing.overload`, or — by the same reasoning — any decorator +pattern that produces multiple `def`s sharing a qualname. + +### MCP Serve-Time Measurements + +Not performed. The DB is in a `FailRun` state with no edges persisted, so +`callers_of`, `execution_paths_from`, `neighborhood`, and the LLM-backed +`summary` / inferred-`callers_of` paths cannot be meaningfully exercised. Doing +the serve pass against a partial DB would produce numbers that do not +characterise the v0.1 surface under the named B.8 slice and would not +characterise the supplementary corpus either (the run did not complete). + +A sanitised rerun against the full corpus minus the 2 overload-using files was +considered and rejected as scope escalation: the methodology's job here is to +faithfully record what `clarion analyze` does against the full elspeth tree, +not to engineer a workaround so the harness can claim "all 7 tools exercised." + +### NFR And Gate Outcome + +| Gate | Target | Outcome | +|---|---|---| +| Analyze completion | run reaches `completed` status | **FAIL**: status `failed` at first duplicate-entity-ID insert | +| Analyze wall-clock | NFR-PERF-01 ≤ 60m | not applicable: aborted at 7m48s | +| Plugin contract: entity-ID uniqueness | ADR-022 implies `{plugin_id}:{kind}:{qualname}` is plugin-unique | **VIOLATED** by the Python plugin under `@typing.overload` | +| Seven-tool end-to-end surface | every tool exercised and useful | not measurable: serve pass not run | +| Summary cache hit rate | NFR-COST-02 ≥ 95% post-stabilisation | not measurable: serve pass not run | +| Cost per consultation | NFR-COST-01 (reframed) | not measurable: serve pass not run | +| Filigree HTTP integration | real reverse route, measured RTT | not exercised | + +### Decision + +The gate is **RED for the supplementary measurement** with a clearly named +mechanism: `@typing.overload` collides with the entity-ID invariant in the +Python plugin. This does not change the Sprint-2-close [2026-05-17T22:43Z +GREEN](#2026-05-17t2243z--green-rerun-superseding-red) verdict on the named B.8 +slice (`/home/john/elspeth/tests`), which exercised all seven MCP tools end to +end. It does name a concrete v0.1 blocker for analyze against any real-world +Python `src/` tree. + +Action: filed `clarion-e29402d1ba` (P2 bug, `wp:3` / `release:v0.1` / +`sprint:2`) with the root cause, fix sketch (PEP 484 semantics — collapse +overload stubs into the implementation entity), and explicit scope note that +the pattern will also surface for `@functools.singledispatch.register` and +similar decorators. The bug should be fixed before the full elspeth checkout +can serve as a B.4* / B.8 stress target. + +Per the pre-written [rollback playbook](./b8-scale-test.md) §4 Red options, +this is **Red option 4** at the supplementary level only — defer the full +elspeth proof. Sprint 2 close stays as the previously recorded measured-partial +milestone on the named slice; the full checkout proof opens a new follow-up +under `clarion-e29402d1ba`. + +## 2026-05-17T21:56Z — RED + +verdict: **RED** + +selected_playbook_option: **Red option 4 — defer the full elspeth proof and close +only a slice demo if Sprint 2 must preserve a partial milestone.** + +rollback_action: + +- Sprint 2 is closed as a measured partial milestone, not MVP-ready. +- Storage-backed MCP navigation is accepted as measured on the elspeth-slice. +- LLM-backed MCP proof (`summary`, inferred `callers_of`) slips to v0.2 repair. +- Follow-up filed: `clarion-ac5f9bf35b` — OpenRouter-backed summary and inferred + MCP paths return invalid JSON. + +reason: `clarion analyze` completed within the v0.1 scale envelope and the +storage-backed MCP tools returned useful bounded responses, but every live +OpenRouter-backed `summary()` call and every inferred-confidence dispatch failed +with `llm-invalid-json`. The B.8 "all 7 tools" proof is therefore not true, and +the NFR-COST-02 summary-cache hit-rate target is unmeasurable rather than green. + +### Reproducibility + +| Field | Value | +|---|---| +| Clarion branch at run | `sprint-2/b8-scale-test` | +| Clarion commit at run | `80a6af9` | +| Corpus source | `/home/john/elspeth/tests` | +| Corpus commit | `deab8f5b21335f37e72ed70fb494a30e2c237b21` | +| Corpus dirty state | one unrelated untracked doc: `docs/superpowers/plans/2026-05-18-report-assemble-aggregation.md` | +| Scratch corpus path | `/tmp/clarion-b8-elspeth-tests-20260517T2156Z` | +| Python files | 1,037 | +| Python LOC | 429,870 | +| Raw artifacts | `tests/perf/b8_scale_test/results/2026-05-17T2156Z/` | +| Analyze command | `target/release/clarion analyze /tmp/clarion-b8-elspeth-tests-20260517T2156Z` | +| Serve driver | `tests/perf/b8_scale_test/driver.py` | +| Serve config | `/tmp/clarion-b8-elspeth-tests-20260517T2156Z/clarion-b8-live.yaml` | +| Filigree route | real dashboard at `http://127.0.0.1:9388/api/entity-associations` | + +This was the representative elspeth-slice requested by B.8, not the fallback +synthetic augmentation. The scratch copy preserved Python file layout and +excluded non-Python files. + +### Analyze-Time Measurements + +| Measurement | Value | +|---|---:| +| Run id | `2c1191ee-294d-472e-90ea-d73173da8368` | +| Status | `completed` | +| Total wall-clock | 447.154s / 7m27s | +| NFR-PERF-01 limit | 60m | +| Peak RSS | 2,033,442,816 bytes / 1,939.242 MiB | +| `.clarion/clarion.db` size | 173 MiB | +| `.clarion/` size at close | 173 MiB | +| Discovery/source walk | ~0.002s from first log to `source tree walk complete` | +| Plugin processing | ~441.346s from `processing plugin` to host findings | +| Commit/close flush | ~5.699s from host findings to `plugin complete` | +| Per-file analysis wall average | ~425.6 ms/file, derived from plugin processing / 1,037 files | +| Pyright per-file p50 | not surfaced by current run stats | +| Pyright per-file p95 | 1,108 ms | +| Pyright AST-index parse p95 | not surfaced in this run; added as `runs.stats.pyright_index_parse_latency_p95_ms` by follow-up `clarion-7aee45d920` | +| Extractor AST parse p95 | not surfaced in this run; added as `runs.stats.extractor_parse_latency_p95_ms` by follow-up `clarion-7aee45d920` | +| Pyright restart count | not surfaced by current run stats | + +Entities by kind: + +| Kind | Count | +|---|---:| +| `class` | 4,378 | +| `function` | 21,399 | +| `module` | 1,036 | +| **Total** | **26,813** | + +Edges by kind and confidence: + +| Kind | Confidence | Count | +|---|---|---:| +| `calls` | `resolved` | 14,327 | +| `contains` | `resolved` | 25,777 | +| `references` | `resolved` | 3,877 | +| **Total** | | **45,369** | + +Run counters: + +| Counter | Value | +|---|---:| +| `dropped_edges_total` | 1,388 | +| `ambiguous_edges_total` | 0 | +| `unresolved_call_sites_total` | 90,178 | +| `entity_unresolved_call_sites` rows | 88,010 | +| `reference_sites_total` | 44,927 | +| `references_resolved_total` | 5,121 | +| `unresolved_reference_sites_total` | 39,806 | +| `references_skipped_external_total` | 21,470 | +| `references_skipped_cap_total` | 0 | +| `findings` table rows | 0 | + +Analyze findings emitted by code: + +| Code | Count | Materiality | +|---|---:|---| +| `CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE` | 8 | Material follow-up signal; overlong `callee_expr` entries are dropped from the unresolved-site side table | +| `CLA-PY-PYRIGHT-*` | 0 | No pyright lifecycle finding surfaced | + +### B.4* Extrapolation Check + +The B.4* mini-gate projected elspeth-full from 828 functions and 3.990s: + +| Basis | Value | +|---|---:| +| Mini function count | 828 | +| Mini wall-clock | 3.990s | +| B.4* named elspeth-full function count | 4,157 | +| B.4* projected elspeth-full wall-clock | 20.032s | +| B.8 actual function count | 21,399 | +| Linear projection from mini to B.8 actual functions | ~103.1s | +| B.8 actual wall-clock | 447.154s | +| Actual / linear projection | ~4.34x slower | + +The extrapolation was directionally useful for unresolved-site growth +(`90,178 / 3,447 ~= 26.2x`; function growth was `21,399 / 828 ~= 25.8x`) but +understated wall-clock materially. This is a yellow analyze signal by itself, +not a red analyze signal, because the run still completed far inside the +60-minute NFR. + +### MCP Serve-Time Measurements + +Driver output: `tests/perf/b8_scale_test/results/2026-05-17T2156Z/mcp-driver-output.json`. +Raw LLM error probe: `tests/perf/b8_scale_test/results/2026-05-17T2156Z/mcp-raw-error-probe.json`. + +The driver exercised all seven tools listed by `tools/list`: + +- `entity_at` +- `find_entity` +- `callers_of` +- `execution_paths_from` +- `summary` +- `issues_for` +- `neighborhood` + +Driver totals: + +| Measurement | Value | +|---|---:| +| Initialize latency | 10.969 ms | +| `tools/list` latency | 0.147 ms | +| Tool calls | 100 | +| OK tool envelopes | 82 | +| Error tool envelopes | 18 | +| Unavailable envelopes | 0 | +| Useful-result calls | 78 | +| Max latency | 16,956.335 ms | +| Overall p50 latency | 2.086 ms | +| Overall p95 latency | 14,493.794 ms | +| Overall p50 response size | 1.039 KiB | +| Overall p95 response size | 2.588 KiB | + +Pattern summary: + +| Pattern | Calls | OK | Errors | Useful | p50 ms | p95 ms | Summary cache hit rate | +|---|---:|---:|---:|---:|---:|---:|---:| +| Light | 5 | 5 | 0 | 5 | 1.082 | 3.517 | n/a | +| Medium cold | 20 | 17 | 3 | 16 | 1.945 | 15,470.175 | unmeasurable | +| Medium warm | 20 | 17 | 3 | 16 | 1.723 | 11,875.340 | unmeasurable | +| Heavy | 50 | 43 | 7 | 41 | 2.106 | 12,324.184 | unmeasurable | +| Inferred edge | 5 | 0 | 5 | 0 | 16,134.971 | 16,956.335 | n/a | + +Per-tool summary: + +| Tool | Calls | OK | Errors | Useful | p50 ms | p95 ms | p95 response KiB | +|---|---:|---:|---:|---:|---:|---:|---:| +| `entity_at` | 16 | 16 | 0 | 16 | 0.220 | 0.652 | 0.711 | +| `find_entity` | 15 | 15 | 0 | 15 | 0.528 | 1.082 | 1.188 | +| `callers_of` | 20 | 15 | 5 | 15 | 3.517 | 16,956.335 | 4.177 | +| `execution_paths_from` | 13 | 13 | 0 | 13 | 0.262 | 0.337 | 1.218 | +| `summary` | 13 | 0 | 13 | 0 | 11,633.245 | 15,470.175 | 0.329 | +| `issues_for` | 9 | 9 | 0 | 5 | 2.728 | 3.262 | 1.215 | +| `neighborhood` | 14 | 14 | 0 | 14 | 3.486 | 7.439 | 2.148 | + +Storage-backed gate slice, excluding LLM-backed summary and inferred dispatch: + +| Slice | Calls | OK | Errors | p50 ms | p95 ms | +|---|---:|---:|---:|---:|---:| +| Default storage-backed navigation | 69 | 69 | 0 | <4 ms | <8 ms | + +The harness's raw `steady_state_storage_backed` aggregate includes inferred +`callers_of` because that is still the same MCP tool name; its p95 is therefore +red. The explicit default-storage slice above is included to preserve the +useful distinction: persisted navigation is healthy, but LLM-backed inferred +dispatch is not. + +### Filigree HTTP Cost At Scale + +The run used the real Filigree dashboard route and a live entity association +attached to `clarion-6222134e0d` for: + +`python:class:e2e.audit.test_attributability.TestAttributability` + +`issues_for` measurements: + +| Measurement | Value | +|---|---:| +| Calls | 9 | +| OK | 9 | +| p50 latency | 2.728 ms | +| p95 latency | 3.262 ms | +| Matched-issue calls | 5 | +| Empty-result calls | 4 | +| Filigree HTTP requests per matched include-contained call | 4 | +| Filigree HTTP requests per direct-only empty call | 1 | + +This validates the ADR-029 reverse-route shape at B.8 scale. No pagination or +cap pressure appeared in this run. + +### OpenRouter Token And Cost Record + +| Measurement | Value | +|---|---:| +| Live summary dispatches attempted | 13 | +| Live inferred dispatches attempted | 5 | +| Successful LLM-backed responses | 0 | +| `summary_cache` rows after run | 0 | +| `inferred_edge_cache` rows after run | 0 | +| Clarion-reported prompt tokens | 0 | +| Clarion-reported completion tokens | 0 | +| Clarion-reported total tokens | 0 | +| Estimated dollar cost | not computable from Clarion artifacts | + +The token/cost ceiling could not be validated. This does not mean the run was +free; it means the provider path returned text that failed Clarion's JSON +contract before the MCP envelope surfaced usage accounting. The v0.2 follow-up +must either enforce JSON-mode/provider constraints or preserve usage tokens even +when the semantic JSON parse fails. + +Raw probes after the driver returned: + +| Probe | Latency | Error | +|---|---:|---| +| `summary(id)` | 12,213.408 ms | `llm-invalid-json`: summary provider returned non-JSON output | +| `callers_of(id, confidence="inferred")` | 14,146.773 ms | `llm-invalid-json`: inferred provider returned invalid JSON at line 1 column 1 | + +### NFR And Gate Outcome + +| Gate | Target | Outcome | +|---|---|---| +| Analyze wall-clock | NFR-PERF-01 <= 60m | PASS: 7m27s | +| Analyze extrapolation | B.4* projection should be verified or disconfirmed | DISCONFIRMED for wall-clock: actual ~4.34x slower than linear mini projection | +| MCP p95 latency | <500ms green, 500ms-2s yellow, >2s red | RED for all-tool p95 due summary/inferred; green for default storage navigation | +| Summary cache hit rate | NFR-COST-02 >=95% post-stabilisation | RED/unmeasurable: every summary call failed, cache rows = 0 | +| Cost per consultation | NFR-COST-01 reframed as operator-facing session cost | RED/unmeasurable: token usage not surfaced on invalid JSON failures | +| Seven-tool end-to-end surface | every tool exercised and useful | RED: 5 storage tools + `issues_for` useful, `summary` not useful, inferred path not useful | +| Filigree HTTP integration | real reverse route, measured RTT | PASS: p95 3.262 ms | + +### Decision + +The gate is **RED**. Sprint 2 cannot honestly be signed as "MVP MCP surface +operational against elspeth scale" because the LLM-backed tool paths fail every +time with the real OpenRouter provider. + +Per the pre-written rollback playbook, Sprint 2 closes only as a partial +milestone. The measurable partial milestone is valuable: + +- elspeth-slice analyze completes under the 60-minute NFR; +- persisted entities/edges are queryable at low latency; +- `entity_at`, `find_entity`, default `callers_of`, `execution_paths_from`, + `issues_for`, and `neighborhood` work against the scale corpus; +- the real Filigree reverse route is fast enough for the B.6 `issues_for` design. + +What slips: + +- live OpenRouter-backed `summary()` correctness; +- summary-cache hit-rate validation; +- inferred-edge LLM dispatch and coalescing-path validation; +- operator-facing token/cost validation for LLM-backed MCP consultations. + +Follow-up issue: `clarion-ac5f9bf35b`. + +## 2026-05-17T22:43Z — GREEN Rerun Superseding RED + +verdict: **GREEN** + +supersedes: **2026-05-17T21:56Z — RED** for the live LLM JSON/cost/cache +blocker tracked as `clarion-ac5f9bf35b`. + +This rerun used the same analyzed elspeth-slice database from the RED entry: +`/tmp/clarion-b8-elspeth-tests-20260517T2156Z/.clarion/clarion.db`. No analyze +rerun was performed; the proof is scoped to the missing `clarion serve` live +OpenRouter/cache evidence. + +Raw artifacts: + +- Cold-cache repair run: `tests/perf/b8_scale_test/results/2026-05-17T2243Z/mcp-driver-output.json` +- Warm-cache steady-state rerun: `tests/perf/b8_scale_test/results/2026-05-17T2243Z/mcp-driver-output-warm-cache.json` + +Clarion source at run time: branch `sprint-2/b8-scale-test`, base commit +`e6bba0f`, with the B.8 repair patch in the working tree. Filigree HTTP was the +real dashboard route at `http://127.0.0.1:9388/api/entity-associations`. + +### Repair Summary + +The live OpenRouter provider now sends strict structured-output requests for +both LLM purposes and uses OpenRouter's broadly supported `max_tokens` +parameter. Invalid semantic JSON paths now preserve token and cost usage in the +MCP envelope; this is covered by regression tests for summary and inferred +dispatch malformed-output paths. + +### Cold-Cache Repair Run + +| Measurement | Value | +|---|---:| +| Tool calls | 100 | +| OK envelopes | 100 | +| Error envelopes | 0 | +| Unavailable envelopes | 0 | +| Useful-result calls | 96 | +| All-tool p50 latency | 1.749 ms | +| All-tool p95 latency | 9,379.681 ms | +| Summary cache rows after run | 3 | +| Inferred edge cache rows after run | 10 | +| Inferred `calls` edges materialized | 57 | + +Summary cache proof: + +| Measurement | Value | +|---|---:| +| Summary calls | 13 | +| Cold misses that wrote cache rows | 3 | +| Warm/cache-hit summary calls | 10 | +| Warm summary hit rate | 100% | +| Driver `summary_miss_then_hit` | true | +| Summary prompt tokens | 4,480 | +| Summary completion tokens | 1,196 | +| Summary total tokens | 5,676 | +| Summary cost | $0.031380 | + +Inferred dispatch proof: + +| Measurement | Value | +|---|---:| +| Inferred `callers_of` tool calls | 5 | +| Inferred dispatch misses | 10 | +| In-run inferred cache hits | 3 | +| Candidate callers considered | 13 | +| Inferred edges materialized | 57 | +| Inferred prompt+completion tokens | 142,585 | +| Inferred cost | $0.503091 | + +Per-tool usefulness in the cold-cache run: + +| Tool | Calls | OK | Errors | Useful | +|---|---:|---:|---:|---:| +| `entity_at` | 16 | 16 | 0 | 16 | +| `find_entity` | 15 | 15 | 0 | 15 | +| `callers_of` | 20 | 20 | 0 | 20 | +| `execution_paths_from` | 13 | 13 | 0 | 13 | +| `summary` | 13 | 13 | 0 | 13 | +| `issues_for` | 9 | 9 | 0 | 5 | +| `neighborhood` | 14 | 14 | 0 | 14 | + +`issues_for` used the real Filigree reverse route and remained fast: + +| Measurement | Value | +|---|---:| +| Calls | 9 | +| OK | 9 | +| p50 latency | 1.801 ms | +| p95 latency | 3.545 ms | +| Matched-issue calls | 5 | + +The cold all-tool p95 is intentionally not the steady-state gate signal because +it includes first-time live OpenRouter calls. It is retained as cost/latency +evidence for cache population. + +### Warm-Cache Steady-State Rerun + +The warm-cache rerun was executed without clearing `summary_cache`, +`inferred_edge_cache`, or materialized inferred edges after the cold-cache run. + +| Measurement | Value | +|---|---:| +| Tool calls | 100 | +| OK envelopes | 100 | +| Error envelopes | 0 | +| Unavailable envelopes | 0 | +| All-tool p50 latency | 1.759 ms | +| All-tool p95 latency | 200.273 ms | +| All-tool max latency | 1,996.851 ms | +| Summary cache hit rate | 100% | +| New LLM tokens | 0 | +| New LLM cost | $0.000000 | + +Warm summary and inferred-cache checks: + +| Check | Value | +|---|---:| +| Summary hits / summary calls | 13 / 13 | +| Warm-labeled summary hits / warm-labeled calls | 10 / 10 | +| Inferred dispatch misses | 0 | +| Inferred cache hits reported | 13 | +| Inferred cached p95 latency | 1,996.851 ms | +| Medium-warm pattern p95 | 4.463 ms | +| Heavy pattern p95 | 4.294 ms | + +The warm all-tool p95 is green under the `<500 ms` target. Cached inferred +dispatch p95 is yellow but inside the `500 ms-2 s` boundary; it performs no new +LLM calls and reports zero token/cost deltas. + +### NFR And Gate Outcome + +| Gate | Target | Outcome | +|---|---|---| +| Analyze wall-clock | NFR-PERF-01 <= 60m | PASS from RED run: 7m27s on the same DB | +| Live summary JSON contract | `summary()` returns parseable contract JSON | PASS: 13/13 summary calls OK, strict fields present | +| Summary cache hit rate | NFR-COST-02 >=95% post-stabilisation | PASS: 10/10 warm-labeled hits in cold run; 13/13 hits in warm rerun | +| Inferred dispatch | Materializes or cleanly caches inferred results | PASS: 57 inferred edges, 10 inferred cache rows, 0 warm misses | +| Cost/tokens on invalid LLM output | Operator-facing evidence even on semantic parse failure | PASS: regression tests cover malformed summary and inferred output stats | +| Seven-tool end-to-end surface | every tool exercised and useful | PASS: all seven tools OK; every tool produced useful results | +| Warm steady-state p95 | <500ms green, 500ms-2s yellow | PASS: all-tool warm p95 200.273 ms green; cached inferred p95 1,996.851 ms yellow | +| Filigree HTTP integration | real reverse route, measured RTT | PASS: p95 3.545 ms | + +The B.4* extrapolation caveat remains a **yellow follow-up**: actual analyze +wall-clock was still ~4.34x slower than the mini-gate's linear projection, even +though the measured analyze run stayed comfortably inside the v0.1 60-minute +envelope. diff --git a/docs/implementation/sprint-2/scope-amendment-2026-05.md b/docs/implementation/sprint-2/scope-amendment-2026-05.md index 9837aeea..22252dcc 100644 --- a/docs/implementation/sprint-2/scope-amendment-2026-05.md +++ b/docs/implementation/sprint-2/scope-amendment-2026-05.md @@ -1,6 +1,6 @@ # Sprint 2 — Mid-Sprint Scope Amendment -**Status**: ACCEPTED — Sprint 2 resumes under this amended scope; B.4* complete (see [B.4* exit criteria §9](./b4-calls-edges.md#9-exit-criteria-panel-revised)) +**Status**: Sprint 2 closed — RED partial milestone; see [signoffs.md](./signoffs.md) and [b8-results.md](./b8-results.md). **Date opened**: 2026-05-16 **Author**: John Morrissey **Predecessor**: [`docs/superpowers/handoffs/2026-04-30-sprint-2-kickoff.md`](../../superpowers/handoffs/2026-04-30-sprint-2-kickoff.md) diff --git a/docs/implementation/sprint-2/signoffs.md b/docs/implementation/sprint-2/signoffs.md new file mode 100644 index 00000000..bc169ac1 --- /dev/null +++ b/docs/implementation/sprint-2/signoffs.md @@ -0,0 +1,133 @@ +# Clarion Sprint 2 — Sign-off Ladder + +**Status**: CLOSED — GREEN after B.8 repair rerun +**Scope**: B.3, B.4*, B.5*, B.6, B.7, B.8 from +[`scope-amendment-2026-05.md`](./scope-amendment-2026-05.md) +**Read-with**: [`b8-results.md`](./b8-results.md), [`../sprint-1/signoffs.md`](../sprint-1/signoffs.md) + +This document originally closed Sprint 2 as a measured RED partial milestone at +commit `e6bba0f` / tag `v0.1-sprint-2`. The post-close B.8 repair issue +`clarion-ac5f9bf35b` is now fixed and closed. The GREEN rerun in +[`b8-results.md`](./b8-results.md#2026-05-17t2243z--green-rerun-superseding-red) +supersedes the RED verdict for live OpenRouter JSON, cost, and cache proof. +Sprint 2 now certifies the seven-tool v0.1 MVP MCP surface against the +representative elspeth-slice, with the B.4* extrapolation caveat retained as a +yellow follow-up. + +Each tick below carries a verifiable artifact: a commit hash, panel record, +result memo, or Filigree issue closeout. + +--- + +## Tier A — Sprint 2 Close + +Every work-package below is closed for Sprint 2 accounting. B.8 first closed RED +and then moved to GREEN through the post-close repair issue; both checkpoints +remain part of the audit trail. + +### A.1 B.3 — Contains Edges + +- [x] **Design doc commit**: `5c510f1` (`docs(wp3): B.3 design — contains edges (first edge kind)`). +- [x] **Implementation range**: `ba9d178` → `50503be` (schema PK cleanup, edge writer command, RawEdge plumbing, contains emission, ontology v0.3.0, parity/e2e/stat fixes). +- [x] **Panel record**: [`b3-contains-edges.md`](./b3-contains-edges.md) design record and incorporated amendments. +- [x] **Exit criteria attestation**: Filigree `clarion-39bc17bde8` closed `done`; close reason records contains-edge row, `edges_inserted == 1`, and `dropped_edges_total == 0` in walking-skeleton verification. + +### A.2 B.4* — Calls Edges And Confidence Tiers + +- [x] **Design doc commit**: `1a112af` (`docs(sprint-2): B.4* design — calls edges via pyright + confidence tiers`). +- [x] **Implementation range**: `e197894` → `4f1197e` (confidence column/index, contract enforcement, pyright session, call resolver, ontology v0.4.0, parity/e2e, gate freshness, B.8 rollback pre-write). +- [x] **Panel record**: [`b4-calls-edges.md` §11](./b4-calls-edges.md#11-panel-review-record). +- [x] **Exit criteria attestation**: Filigree `clarion-2d2d1d27b5` closed `done`; close note records ADR-023 gates green and B.4* week-2 gate `GREEN` in [`b4-gate-results.md`](./b4-gate-results.md). + +### A.3 B.5* — References Edges + +- [x] **Design doc commit**: `95c9a5e` (`docs(wp3): design B.5 references edges via pyright`). +- [x] **Implementation range**: `6226543` → `3ed6c89` (references contract, lexical-owner collection, pyright definitions, stats, public surface, review-gap fixes). +- [x] **Panel record**: [`b5-references-edges.md`](./b5-references-edges.md) panel-reviewed design and review follow-up notes. +- [x] **Exit criteria attestation**: Filigree `clarion-b0cedfd2bb` closed `done`; close reason names commit `3ed6c89` and the GREEN scale-smoke artifact. + +### A.4 B.6 — Seven-Tool MCP Surface + +- [x] **Design doc commit**: `6a9a7b2` (`docs(wp8): design B.6 MCP surface`). +- [x] **Implementation range**: `b0a12a6` → `a53d2e4` (MCP stdio server, `clarion serve`, storage-backed tools, summary cache, inferred dispatch, `issues_for`, e2e observability, OpenRouter provider swap). +- [x] **Panel record**: [`b6-mcp-surface.md`](./b6-mcp-surface.md) Stage 0 panel record and reconciliation. +- [x] **Exit criteria attestation**: Filigree `clarion-e2a3672cc9` closed `done`; B.6 local gates passed with RecordingProvider coverage, not live-provider proof. + +### A.5 B.7 — Entity Associations Binding + +- [x] **Design source**: [ADR-029](../../clarion/adr/ADR-029-entity-associations-binding.md) and B.6 `issues_for` integration design. +- [x] **Implementation artifacts**: Filigree PR 42 merged; Clarion-side `issues_for` integration commits include `16634ae` and `29d3865`. +- [x] **Panel record**: ADR-029 federation audit and B.6 Filigree reverse-route review. +- [x] **Exit criteria attestation**: Filigree `clarion-73ab0da435` closed `done`; B.8 measured the real reverse route at p95 3.262 ms. + +### A.6 B.8 — Elspeth Scale-Test + +- [x] **Test-plan commit**: `5a396a5` (`test(perf): add B.8 scale-test plan and harness`). +- [x] **Harness correction commit**: `80a6af9` (`test(perf): mark B.8 heavy samples steady-state`). +- [x] **Reviewer panel record**: [`b8-elspeth-scale-test.md` §7](./b8-elspeth-scale-test.md#7-reviewer-panel-record). +- [x] **Historical RED result memo commit**: `ad2ef80` (`docs(sprint-2): record B.8 red scale-test results`). +- [x] **Historical RED signoff commit**: `e6bba0f` (`docs(sprint-2): close Sprint 2 signoff ladder`), tagged `v0.1-sprint-2`. +- [x] **Repair implementation commit**: `ab6b1dd` (`fix(wp3): OpenRouter strict-JSON path for B.8 green rerun`). +- [x] **GREEN rerun attestation**: [`b8-results.md`](./b8-results.md#2026-05-17t2243z--green-rerun-superseding-red) records the cold and warm OpenRouter-backed reruns on the same analyzed DB. The cold run produced 100/100 OK MCP calls, 3 summary cache rows, 10 inferred edge cache rows, and 57 materialized inferred `calls` edges. The warm rerun produced 100/100 OK calls, all-tool p95 200.273 ms, summary cache hit rate 100%, and zero new token/cost delta. +- [x] **Repair follow-up closure**: Filigree `clarion-ac5f9bf35b` closed `closed`; close verification names the B.8 GREEN artifacts and the malformed-output regression coverage. + +--- + +## Sprint 2 Close Verdict + +**Gate label**: GREEN after repair. + +**What is signed off**: + +- elspeth-slice analyze completed in 7m27s with 26,813 entities and 45,369 edges. +- Storage-backed MCP navigation was operational and low-latency at scale. +- All seven MCP tools returned OK and useful results in the GREEN cold-cache rerun. +- Live OpenRouter-backed `summary()` returned strict JSON, populated the summary cache, and reached 100% warm cache hits. +- Live inferred dispatch materialized inferred `calls` edges, populated `inferred_edge_cache`, and returned zero new token/cost deltas in the warm rerun. +- `issues_for` used the real Filigree reverse route and returned matched data. +- The B.8 harness and raw cold/warm measurements are committed and reusable. + +**Remaining caveats**: + +- The B.4* mini-gate wall-clock extrapolation was materially optimistic: the B.8 analyze run was ~4.34x slower than the mini-gate's linear projection, even though it remained well inside NFR-PERF-01. +- This signoff certifies the representative elspeth-slice, not a full-repository elspeth proof. +- Non-umbrella Sprint-2 audit/follow-up issues remain open by design and are not part of this close ladder. + +**Repair closure**: the live OpenRouter-backed `summary()` correctness, +inferred-edge JSON-contract reliability, and cost/cache validation gaps from the +RED close are repaired by `clarion-ac5f9bf35b`. Broader v0.1/v0.2 deferrals +remain as recorded in the scope amendment. + +--- + +## Tracker State + +Sprint-2 umbrella issues verified at close: + +| Issue | Work package | Status | +|---|---|---| +| `clarion-39bc17bde8` | B.3 | `done` | +| `clarion-2d2d1d27b5` | B.4* | `done` | +| `clarion-b0cedfd2bb` | B.5* | `done` | +| `clarion-e2a3672cc9` | B.6 | `done` | +| `clarion-73ab0da435` | B.7 | `done` | +| `clarion-6222134e0d` | B.8 | `done`; historical close fields record RED | +| `clarion-ac5f9bf35b` | B.8 repair follow-up | `closed`; GREEN rerun verified | + +Non-umbrella Sprint-2 audit/follow-up issues remain open by design; they are not +part of this close ladder. + +--- + +## Tags + +The existing `v0.1-sprint-2` tag points at the historical RED close commit +`e6bba0f`: + +```bash +git tag v0.1-sprint-2 -m "Sprint 2 close — MVP MCP surface against elspeth scale-test" +``` + +Do **not** move that tag. It is referenceable as the original close checkpoint. +The post-repair GREEN evidence lives after the tag, in commit `ab6b1dd` and the +GREEN rerun section of [`b8-results.md`](./b8-results.md#2026-05-17t2243z--green-rerun-superseding-red). diff --git a/docs/implementation/v0.1-plan.md b/docs/implementation/v0.1-plan.md index 04be0db9..da988175 100644 --- a/docs/implementation/v0.1-plan.md +++ b/docs/implementation/v0.1-plan.md @@ -299,8 +299,9 @@ qualnames Clarion translates). - Call-graph precision sufficient for the cross-cutting findings in WP4 (intra-module resolved; inter-module resolved when import resolution succeeded). - Structural finding emission for the Python rule catalogue in `detailed-design.md` §5. -- Identity reconciliation hooks per ADR-018: produce qualnames in the form Wardline - also produces, so downstream translation is a lookup not a guess. +- Identity reconciliation hooks per ADR-018: produce qualnames in a + Wardline-translatable form, with explicit translation between Clarion's dotted + module prefix and Wardline's separate file-path plus bare-qualname fields. **Out of scope (explicit)**: - Type inference, dataflow, taint (NG-05). diff --git a/docs/implementation/v0.1-publish/thread-1-pre-publish-blockers.md b/docs/implementation/v0.1-publish/thread-1-pre-publish-blockers.md new file mode 100644 index 00000000..2b9a84a5 --- /dev/null +++ b/docs/implementation/v0.1-publish/thread-1-pre-publish-blockers.md @@ -0,0 +1,433 @@ +# Thread 1 — Pre-publish blockers (program of work) + +> **For agentic workers:** REQUIRED SUB-SKILL: `superpowers:subagent-driven-development` (recommended) or `superpowers:executing-plans`. Each workstream is independently dispatchable; sequencing is described in §1. + +**Status**: drafted 2026-05-18 — not yet broken into Filigree issues. +**Predecessor context**: Sprint 2 closed GREEN ([`../sprint-2/signoffs.md`](../sprint-2/signoffs.md)); the 2026-05-18 codebase archaeology ([`../../arch-analysis-2026-05-18-1244/04-final-report.md`](../../arch-analysis-2026-05-18-1244/04-final-report.md)) is the authoritative current-state snapshot. +**Goal**: take the amended-v0.1 MCP-MVP from "works on the elspeth-slice corpus on the author's box" to "publishable v0.1" — meaning *an outside operator can install it, point it at an arbitrary repo without leaking secrets, and find their way to first value in five minutes*. + +**Scope discipline**: this is *only* Thread 1 (pre-publish operational/security blockers). Two adjacent threads exist and are NOT in this program: + +- **Thread 2** — reconcile `CON-FILIGREE-02` ("Filigree `registry_backend` is a hard v0.1 dependency") against the 2026-05 scope amendment (deferred WP9-B + WP10 to v0.2). One-day editorial pass in `requirements.md` + amendment memo; out of scope here. +- **Thread 3** — dogfood pass: `clarion analyze` + reproduce the arch-analysis findings via the 7 MCP tools against Clarion / Filigree / Wardline themselves. Out of scope here. + +--- + +## 1. Workstream map and sequencing + +Four workstreams. **A** is the only one with significant engineering weight; **B/C** are mostly docs + packaging; **D** is the verification gate that proves A/B/C composed correctly. + +``` +A WP5 pre-ingest secret scanner ─────────────────────┐ +B Operator-facing entry surface ─────────────────────┤ +C Distribution mechanics + clarion install --force ──┤ + ↓ + D External-operator smoke test (gate) +``` + +**A** ships in parallel with **B** and **C**: the scanner is a `clarion-core`-internal change; the docs / packaging touch repo-root + CI + plugin manifests. No file-level collisions expected. + +**D** is the publish gate. Until D is green on a fresh VM, no `v0.1` tag. + +**Effort estimate** (single engineer, agentic velocity): **A** ≈ 6–9 working days; **B** ≈ 1–2 days; **C** ≈ 2–4 days (depending on chosen distribution path); **D** ≈ 1 day. Total: ~3 weeks elapsed if serialised, ~2 weeks if **B/C** run in parallel behind **A**. + +**Filigree umbrellas to create** before kickoff: + +| Umbrella | Title | Labels | +|---|---|---| +| WP5 umbrella | `WP5 — Pre-ingest secret scanner (ADR-013)` | `release:v0.1`, `sprint:3`, `wp:5`, `adr:013`, `tier:a` | +| Repo-UX umbrella | `Publish-prep — operator-facing entry surface` | `release:v0.1`, `sprint:3`, `docs`, `tier:a` | +| Distribution umbrella | `Publish-prep — distribution + install ergonomics` | `release:v0.1`, `sprint:3`, `tier:a` | +| Publish gate | `Publish gate — external-operator smoke test` | `release:v0.1`, `sprint:3`, `tier:a` | + +The L-* arch-analysis items already in flight (L-1 `--force`, L-7 blank actor, etc.) fold into Workstream C as named subtasks (§4); do **not** double-file. + +--- + +## 2. Workstream A — WP5 Pre-ingest secret scanner + +### A.0 Spec source + +[ADR-013](../../clarion/adr/ADR-013-pre-ingest-secret-scanner.md) fully specifies behaviour, rule set, baseline format, override semantics, and plugin-boundary interaction. It is Accepted; do not re-litigate. The `system-design.md` §10 paragraph this ADR formalises was retained when ADR-013 was authored. + +The requirements floor: + +- `NFR-SEC-01` — pre-ingest scan + block + baseline whitelist +- `NFR-SEC-04` — security events as findings (audit surface) +- `NFR-OPS-01` / `NFR-OPS-04` — single-binary distribution (rules out the Python `detect-secrets` embed; ADR-013 §Alternative 1 is the dispositive read) + +### A.1 Crate layout decision + +**Decision required at A.1**: does the scanner ship as a new sibling crate `crates/clarion-scanner/`, or as a `clarion-core::secret_scanner` module? + +**Recommendation**: new sibling crate `crates/clarion-scanner/`. Reasons: +1. ADR-013 calls out the implementation as `clarion_scanner` crate (line 40); use the name the ADR uses. +2. The rule set is data-heavy (regex tables + entropy tuning) and benefits from being a leaf crate with no `tokio` / `rusqlite` deps. +3. Keeps `clarion-core/src/plugin/host.rs` from growing further (currently 3 126 LOC; arch-analysis §5.4 A-3 named this an accepted-but-watched risk). + +The CLI consumes it via `clarion-cli/src/analyze.rs` directly; the writer-actor never sees it (findings flow through the existing `HostFinding` → `WriterCmd::InsertEntity` path with `properties.briefing_blocked = "secret_present"` plus a `CLA-SEC-SECRET-DETECTED` finding row). + +### A.2 Task breakdown + +Tasks are sized to fit a single agent pass each (≤ ~500 LOC plus tests). They sequence top-to-bottom; tasks 1 and 2 can parallelise if dispatched to two agents. + +#### Task 1 — Rule set + pattern registry + +**Files**: +- Create: `crates/clarion-scanner/Cargo.toml` (workspace member) +- Create: `crates/clarion-scanner/src/lib.rs`, `src/patterns.rs`, `src/entropy.rs` +- Modify: `Cargo.toml` (workspace root — add `crates/clarion-scanner`) + +**Scope**: implement the named-credential regex table from ADR-013 lines 35–38 (AWS, GitHub, Anthropic, OpenAI, Stripe, Slack, JWT, private-key headers, contextual-credential names). Implement Shannon entropy over a byte slice. Public surface: + +```rust +pub struct Scanner { /* compiled regex set + entropy thresholds */ } +pub struct Detection { + pub rule_id: &'static str, // e.g. "AwsAccessKeyId", "HighEntropyBase64" + pub category: SecretCategory, // for the CLA-SEC- finding mapping + pub byte_offset: usize, + pub line_number: u32, + pub matched_len: usize, // never persist the literal bytes + pub hashed_secret: [u8; 20], // sha1, baseline-compat +} +impl Scanner { + pub fn new() -> Self; // default thresholds per ADR-013 + pub fn scan_bytes(&self, buf: &[u8]) -> Vec; +} +``` + +**Tests**: one positive + one negative fixture per rule (AWS access key, GitHub PAT, RSA private-key header, etc.). For high-entropy detection: a 32-char base64-looking string passes; a UUID fails. Fixtures live in `crates/clarion-scanner/tests/fixtures/`. + +**Exit**: `cargo test -p clarion-scanner` green; clippy `-D warnings` clean; the crate compiles with no `tokio` / `rusqlite` / `serde_norway` deps (assert via `cargo tree -p clarion-scanner | head -30`). + +#### Task 2 — Baseline parser (`.clarion/secrets-baseline.yaml`) + +**Files**: +- Create: `crates/clarion-scanner/src/baseline.rs` +- Modify: `crates/clarion-scanner/src/lib.rs` (re-export) + +**Scope**: parse the `detect-secrets` v1.x baseline schema (ADR-013 lines 60–68). Required schema fields: `version` (must equal `"1.0"`), `results` (map of relative-path → list of `{type, hashed_secret, line_number, is_secret, justification}`). The `justification` field is required (ADR-013 line 71). Missing → emit `CLA-INFRA-SECRET-BASELINE-NO-JUSTIFICATION` (rule constant in `clarion-scanner` consumed by the CLI). + +Use `serde_norway` (already a workspace dep; replaces `serde_yaml` per commit `9ffc5c8`). Match-then-suppress at `Detection` granularity, keyed on `(file_path, hashed_secret, line_number)`. Provide: + +```rust +pub fn load_baseline(path: &Path) -> Result; +pub fn suppress(detections: Vec, baseline: &Baseline, file: &Path) -> SuppressionResult; +``` + +Where `SuppressionResult { allowed: Vec, suppressed: Vec }` — both retained so the CLI can emit `CLA-SEC-SECRET-DETECTED` for unsuppressed *and* a `CLA-INFRA-SECRET-BASELINE-MATCH` info-level finding when a baseline entry actually fires (audit surface per `NFR-SEC-04`). + +**Tests**: fixture baseline file + scanner output → asserts allowed/suppressed partitioning; fixture missing-justification → returns the expected `BaselineError` variant; baseline path absent → returns an empty baseline (no error). + +**Exit**: `cargo test -p clarion-scanner` green including the baseline module; baseline round-trip test (parse → serialise → parse) byte-identical. + +#### Task 3 — CLI wiring: pre-ingest hook in `analyze::run` + +**Files**: +- Modify: `crates/clarion-cli/src/analyze.rs` +- Modify: `crates/clarion-cli/Cargo.toml` (add `clarion-scanner` dep) +- Create: `crates/clarion-cli/src/secret_scan.rs` (orchestration module — keep `analyze.rs` from growing further per arch-analysis H-1) + +**Scope**: between the source-tree walk (currently `collect_source_files` at `analyze.rs:182`) and the per-plugin processing loop, insert a pre-ingest scan pass. For each file in `source_files`: + +1. Read the file buffer (already needed for `analyze_file` RPC dispatch; this is the natural place — do **not** re-read in the plugin pass). +2. Run `Scanner::scan_bytes`; apply baseline suppression. +3. If `allowed` non-empty: + - Mark the file `briefing_blocked: secret_present` in a `BTreeMap` carried through to the per-plugin pass. + - Accumulate `CLA-SEC-SECRET-DETECTED` findings (one per detection, severity `error`). +4. Files in this map still go to the plugin (structural extraction runs, ADR-013 line 46) but the entities emitted carry `properties.briefing_blocked = "secret_present"`. + +The `briefing_blocked` flag plumbs through `RawEntity.extra` → `EntityRecord.properties_json` → the `entities.properties` column. The MCP `summary` tool already reads `entities.properties` for cache lookup (see `clarion-mcp/src/lib.rs:1010`); add the block check there in Task 5. + +**Tests**: integration test in `crates/clarion-cli/tests/analyze.rs` — fixture project with a `.env` containing a fake AWS key. Assert: +- `analyze` exits 0 (`SoftFailed` — partial success path; arch-analysis H-1 coverage gap). +- `entities` table has rows for the `.env` file's structural entities. +- Those entities' `properties_json` contains `"briefing_blocked":"secret_present"`. +- `findings` table has one `CLA-SEC-SECRET-DETECTED` row referencing that file. + +**Exit**: integration test green; the new `secret_scan.rs` module is < 250 LOC; `analyze.rs` net growth ≤ 30 LOC (delegate to the new module). + +#### Task 4 — Override semantics: `--allow-unredacted-secrets` + +**Files**: +- Modify: `crates/clarion-cli/src/cli.rs` (clap definition) +- Modify: `crates/clarion-cli/src/analyze.rs` + `secret_scan.rs` + +**Scope**: implement the override path per ADR-013 lines 74–82. + +- TTY: prompt with the detection list; require the operator to type the literal string `yes-i-understand`. +- Non-TTY: require both `--allow-unredacted-secrets` AND `--confirm-allow-unredacted-secrets=yes-i-understand`. Anything else → exit non-zero with `CLA-INFRA-SECRET-OVERRIDE-UNCONFIRMED` to stderr (do **not** silently bypass). +- When the override fires for file `F`: F's entities are NOT marked `briefing_blocked`; emit one `CLA-SEC-UNREDACTED-SECRETS-ALLOWED` finding per affected file (severity `error`, audit surface). +- Record `{override_used: true, files_affected: [...]}` in `runs.stats` (the existing `runs.stats` text column). + +**TTY detection**: use `std::io::IsTerminal` on stdin; this is in `std` since Rust 1.70 and the workspace's `rust-toolchain.toml` is well past that. + +**Tests**: +- Non-TTY override-confirmed: secret-bearing fixture + both flags → no `briefing_blocked`, one `CLA-SEC-UNREDACTED-SECRETS-ALLOWED` finding per file. +- Non-TTY override-unconfirmed: only `--allow-unredacted-secrets` → exit code 78 (`EX_CONFIG` per `sysexits.h`; pick once, document in `cli.rs`); `CLA-INFRA-SECRET-OVERRIDE-UNCONFIRMED` finding NOT persisted (run never started); stderr contains the rule-ID for the operator to grep. +- TTY path: separate `expectrl`-style test or skip with a `#[ignore]` and document; TTY behaviour is verified manually in Workstream D. + +**Exit**: integration tests green; the override surface has both happy-path and the "footgun absent confirmation" path covered. + +#### Task 5 — MCP-side awareness of `briefing_blocked` + +**Files**: +- Modify: `crates/clarion-mcp/src/lib.rs` (the `summary` tool dispatch path) +- Modify: `crates/clarion-mcp/tests/storage_tools.rs` + +**Scope**: when `summary(id)` is called on an entity whose `properties.briefing_blocked == "secret_present"`, return an envelope shape (do **not** invoke the LLM, do **not** consume budget): + +```json +{ + "entity_id": "python:function:demo.foo|function", + "summary": null, + "briefing_blocked": "secret_present", + "remediation": "File flagged by pre-ingest secret scan. Fix the secret or whitelist via .clarion/secrets-baseline.yaml; ADR-013." +} +``` + +This is the consult-mode-agent surface for "the absence of a summary is policy, not pipeline failure" (ADR-013 line 49). The four already-existing `issues_unavailable` envelopes in `clarion-mcp::filigree` are the precedent for this envelope shape. + +**Tests**: storage-tools test with a fixture entity flagged `briefing_blocked` → `summary` tool returns the envelope; no row is added to `summary_cache`; the budget ledger is untouched. + +**Exit**: storage-tools test green; manual verification that `RecordingProvider` is NOT invoked on a blocked entity (assert no fixture file is created in the recording-mode test setup). + +#### Task 6 — Rule catalogue entries in `detailed-design.md` + +**Files**: +- Modify: `docs/clarion/v0.1/detailed-design.md` (§5 rule catalogue) + +**Scope**: append rule rows for `CLA-SEC-SECRET-DETECTED`, `CLA-SEC-UNREDACTED-SECRETS-ALLOWED`, `CLA-INFRA-SECRET-BASELINE-NO-JUSTIFICATION`, `CLA-INFRA-SECRET-BASELINE-MATCH`, `CLA-INFRA-SECRET-OVERRIDE-UNCONFIRMED`. Each row: rule-ID, severity, category, one-sentence description, one-sentence remediation, ADR pointer. + +This makes the WP9-B Filigree-emission story (deferred to v0.2) able to round-trip these IDs without a separate spec pass. + +**Exit**: design-doc lint passes (no broken cross-references); ADR-013 retains the canonical authority on *behaviour*, the design doc carries the *catalogue*. + +#### Task 7 — Documentation: operator surface + +**Files**: +- Create: `docs/operator/secret-scanning.md` +- Modify: `docs/operator/README.md` (add link) + +**Scope**: operator-facing doc — what gets blocked, how to whitelist via `.clarion/secrets-baseline.yaml`, what the override does, how to find the audit trail (`findings` table queries, future Filigree integration). One page, ≤ 250 lines. Link from the top-level README (Workstream B Task 1). + +**Exit**: a non-engineer can read this doc and resolve a baseline false-positive without reading ADR-013. + +### A.3 Workstream A exit criteria + +All tasks green; in addition: +- `cargo test --workspace --all-features` passes. +- Existing CI gates (ADR-023 floor) unchanged in pass status. +- A new E2E test under `tests/e2e/` (parallels `sprint_1_walking_skeleton.sh`) runs `clarion install && clarion analyze` against a fixture project containing one known secret and asserts: exit 0, entities present, briefing_blocked flagged, finding persisted. +- The Sprint-1 walking-skeleton E2E continues to pass (no regression on the clean-fixture path). + +--- + +## 3. Workstream B — Operator-facing entry surface + +### B.1 Top-level repo README + +**Files**: +- Create: `README.md` at repo root. + +**Scope**: there is no top-level README currently. The reader-ladder under `docs/suite/briefing.md` → `docs/suite/loom.md` → `docs/clarion/v0.1/README.md` assumes the reader already knows to start there. A first-time visitor (PyPI / crates.io / GitHub front page) has no entry point. + +The README must answer, in order: + +1. **What this is** — one paragraph. Use the briefing's framing ("Clarion is a code-archaeology tool…") but compress to ~80 words. +2. **What it does today** — bullet list of the 7 MCP tools and what each answers, with one example invocation each. +3. **Quick start** — `clarion install && clarion analyze && clarion serve`, with the expected stdout shapes. Link to the operator tutorial (Task B.2). +4. **Status** — explicit "v0.1 — Python only; structural + on-demand LLM summarisation; Filigree finding emission deferred to v0.2." Quote the scope: don't oversell. +5. **Project layout** — three-sentence map (Rust workspace + Python plugin + docs) with links to `docs/clarion/v0.1/README.md` for the design ladder and `docs/clarion/adr/README.md` for the ADR index. +6. **Contributing** — pointer to `CLAUDE.md` and the test commands (ADR-023 floor). + +**Length target**: ≤ 200 lines. No installation instructions deeper than `cargo install ...` + `pipx install clarion-plugin-python` (Workstream C delivers the actual commands). + +**Exit**: a developer who has never seen the repo can answer "is this for me?" in 60 seconds. + +### B.2 Getting-started tutorial + +**Files**: +- Create: `docs/operator/getting-started.md` +- Modify: `docs/operator/README.md` (index) + +**Scope**: a single-flow tutorial: install Clarion, run against a tiny example repo provided in `examples/quickstart-repo/` (or use `crates/clarion-plugin-fixture`'s test inputs — pick one, document), connect a consult-mode agent over MCP, ask one question, see a real answer. Includes: + +- Prerequisite versions (Rust toolchain per `rust-toolchain.toml`; Python 3.11+; `pyright-langserver` 1.1.409 — pinned in the Python plugin manifest). +- Required env vars for live LLM calls (`OPENROUTER_API_KEY`). Note that `clarion analyze` works without the LLM (structural-only); summarisation requires the key. +- The seven MCP tool names with one example each. +- Troubleshooting: plugin not discovered → check `$PATH`; secret block fires → link to `secret-scanning.md`. + +**Exit**: a fresh operator runs through the tutorial start-to-finish in ≤ 15 minutes and gets a non-trivial answer from an agent. + +### B.3 Workstream B exit criteria + +- Top-level `README.md` present and reviewed. +- Getting-started tutorial walked end-to-end by someone who did NOT write it (the publish-gate operator in Workstream D, on a fresh VM). + +--- + +## 4. Workstream C — Distribution + install ergonomics + +### C.1 `clarion install --force` (arch-analysis L-1) + +**Files**: +- Modify: `crates/clarion-cli/src/install.rs`, `src/cli.rs` + +**Scope**: the `--force` flag is declared in the clap definition (`cli.rs:17–18`) and rejected at runtime (`install.rs:87–92`). Wire it up: when set, remove existing `.clarion/` *atomically* (rename-to-tmpdir + remove tmpdir, never partial deletes), then proceed. Refuse if `.clarion/clarion.db` shows a `runs` row with `status='running'` (someone else is using this DB) unless `--force --force` (double-force) is passed — the operator owns the override. + +This closes Filigree issue `clarion-2d178ddda0` (P3, ready). + +**Exit**: integration test in `crates/clarion-cli/tests/install.rs` exercises the three paths (no `.clarion/` → install; `.clarion/` present without `--force` → exit non-zero with helpful message; `.clarion/` present with `--force` → atomic replace, success). + +### C.2 Distribution decision + +**Decision required at C.2**: which packaging path ships v0.1? Three viable options; pick one and ADR it. + +| Option | Rust binary | Python plugin | +|---|---|---| +| (a) Source-only — `cargo install --git` + `pipx install --editable git+https://…` | repo URL | repo URL | +| (b) GitHub Releases — pre-built binaries per platform; plugin sdist attached | `gh release download` + `mv to ~/.cargo/bin/` | `pipx install ./clarion-plugin-python-*.tar.gz` | +| (c) Public registries — `cargo install clarion-cli` (crates.io) + `pipx install clarion-plugin-python` (PyPI) | crates.io | PyPI | + +**Recommendation**: (b) for the v0.1 publish, (c) for v0.2 once names are reserved and the publish cadence is established. Reasons: +- (a) burns ten minutes of cargo compile on every new install — bad first impression. +- (c) requires name reservation on crates.io + PyPI, and version-bump discipline; not free. +- (b) ships in a day with `cargo-dist` or a hand-written GH Actions workflow; the install command is one `curl | tar` away from being scriptable. + +If (b) is chosen, file an ADR (ADR-032 candidate: "v0.1 distribution via GitHub Releases; promote to public registries at v0.2"). The ADR is short — half a page. + +**Files** (if (b) chosen): +- Create: `.github/workflows/release.yml` +- Create: `docs/clarion/adr/ADR-032-v0.1-distribution.md` (or reuse the next free ADR number — check the index) + +**Workflow shape**: +- Trigger: `push: tags: ['v0.1*']`. +- Matrix: `x86_64-unknown-linux-gnu`, `aarch64-apple-darwin`, `x86_64-apple-darwin` minimum. Windows is out of v0.1 scope (no requirement; `setrlimit` is Unix-only — `clarion-core::plugin::limits`). +- Build the `clarion` binary; build the Python plugin sdist (`python -m build --sdist plugins/python`). +- Attach both to the GH release; auto-generate release notes from `git log v0.1-sprint-2..HEAD` filtered to merge commits. + +**Exit**: a tag `v0.1.0` push produces a GH release with downloadable artifacts; a hand-test on a fresh VM (Workstream D) installs from those artifacts successfully. + +### C.3 Plugin auto-discovery affordance + +**Files**: +- Modify: `docs/operator/getting-started.md` (Workstream B Task 2) +- Possibly: `crates/clarion-cli/src/cli.rs` (add a `clarion doctor` subcommand — optional, see below) + +**Scope**: plugin discovery walks `$PATH` looking for `clarion-plugin-*` executables (ADR-002 / L9 convention). For someone running `pipx install clarion-plugin-python`, the plugin lands in `~/.local/bin/` — which is `$PATH` on most Linux but not always on macOS, and is silent when missing. Two paths: + +- Document the `$PATH` requirement crisply in the tutorial. Cheap; punts the problem. +- Add a `clarion doctor` subcommand that prints discovered plugins and a yes/no for "found a Python plugin." Spends a day; the operator gets a self-diagnosis path. + +**Recommendation**: tutorial only for v0.1; `clarion doctor` is a v0.2 nice-to-have. Document the failure mode (zero plugins discovered → `SkippedNoPlugins`, which currently exits 0 — verify and note this). + +### C.4 Workstream C exit criteria + +- `clarion install --force` lands and tests green. +- Distribution decision recorded as an ADR; the chosen path is exercised end-to-end (a release is produced). +- Tutorial documents the installation path that the chosen distribution implies. + +--- + +## 5. Workstream D — Publish gate: external-operator smoke test + +### D.1 Test setup + +**Files**: +- Create: `tests/e2e/external-operator-smoke.md` (manual checklist) — and/or `.github/workflows/external-operator-smoke.yml` if automatable. + +**Scope**: spin up a fresh VM (or container — `ubuntu:24.04` is a fair proxy). Use **only** the installation instructions in `README.md` and `docs/operator/getting-started.md`. No `git clone`, no `cargo build` from source. + +Steps: + +1. Install Rust binary per Workstream C's chosen path. +2. Install Python plugin per the same. +3. `clarion install` against a small public Python project (suggestion: `requests==2.32.x` source tarball — ~7k LOC, well-behaved, no secrets). +4. `clarion analyze` — assert exit 0, non-empty entities count. +5. `clarion serve` in one shell; connect a consult-mode agent via MCP in another (Claude Desktop or `mcptool` CLI — pick one, document). +6. Ask the agent three pre-scripted questions: + - "List the top-level modules in this project." + - "What calls `requests.get`?" + - "Summarise `requests.sessions.Session.send`." (forces a live LLM call → exercises OpenRouter path + budget + cache.) +7. Re-run `analyze` to confirm idempotency (re-walk doesn't double-emit; existing entities updated). +8. Plant a `.env` file containing `AKIA0123456789ABCDEF` in the test project; re-run `analyze`; assert the WP5 block fires + finding persists. + +### D.2 Acceptance + +The smoke test passes if all eight steps complete without operator improvisation. Any step that requires reading source code (rather than the docs) is a Workstream B bug to fix before publish. + +### D.3 Workstream D exit criteria + +- Smoke test executed at least once on each platform the release workflow produces artifacts for. +- The operator who runs it is NOT the author. Recruit a second engineer or use a fresh agent session with no prior repo context. +- Any deviations between docs and reality become Workstream B tickets; cycle until clean. + +--- + +## 6. What this program does NOT cover + +To prevent scope creep mid-execution, the following are explicitly OUT: + +- **WP9-B / WP10** (findings emission to Filigree, registry_backend, SARIF translator) — Thread 2; v0.2 in the amended plan. +- **WP4 phases beyond Phase 1** (clustering, Phase-7 `CLA-*` cross-cutting rules, Phase-8 entity-set diff) — v0.2. +- **WP7 guidance system** — v0.2. +- **Multi-language plugins** — `NG-15`, v0.2+. +- **MCP `summary(id)` module/subsystem aggregation** — `ADR-030` defers to v0.2; v0.1 ships leaf-only. +- **The L-3 through L-8 arch-analysis items** — in flight as separate Filigree issues; pick them up opportunistically but do not block the publish on them. L-1 is named here because it is install-ergonomic; the rest are quality polish, not gate items. + +--- + +## 7. Filigree seeding (suggested first commands) + +```bash +# Workstream A — WP5 umbrella + 7 task issues +filigree create --type=work_package --title="WP5 — Pre-ingest secret scanner (ADR-013)" \ + --labels="release:v0.1,sprint:3,wp:5,adr:013,tier:a" --priority=P1 + +# Then per task; example: +filigree create --type=task --title="WP5 Task 1 — Scanner crate + rule set + entropy" \ + --labels="release:v0.1,sprint:3,wp:5,adr:013,crate:scanner" +# repeat for tasks 2–7 + +# Workstream B +filigree create --type=task --title="Publish-prep: top-level README" --labels="release:v0.1,sprint:3,docs" +filigree create --type=task --title="Publish-prep: getting-started tutorial" --labels="release:v0.1,sprint:3,docs" + +# Workstream C +filigree create --type=task --title="Publish-prep: clarion install --force" --labels="release:v0.1,sprint:3,crate:cli" +# (Folds in clarion-2d178ddda0; close that with a forward-pointer.) +filigree create --type=task --title="Publish-prep: choose v0.1 distribution path + ADR + release workflow" \ + --labels="release:v0.1,sprint:3" + +# Workstream D +filigree create --type=task --title="Publish gate: external-operator smoke test on fresh VM" \ + --labels="release:v0.1,sprint:3,tier:a" --priority=P1 +``` + +Set the dependencies: + +```bash +# A blocks D +filigree add-dep --blocked-by +# B blocks D +filigree add-dep --blocked-by --blocked-by +# C blocks D +filigree add-dep --blocked-by +# C --force task supersedes the standalone L-1 +filigree close clarion-2d178ddda0 --reason="superseded by Publish-prep --force task " +``` + +--- + +## 8. References + +- [ADR-013 — Pre-ingest secret scanner with LLM-dispatch block](../../clarion/adr/ADR-013-pre-ingest-secret-scanner.md) +- [ADR-007 — Summary cache key (briefing_blocked semantics)](../../clarion/adr/ADR-007-summary-cache-key.md) +- [ADR-021 — Plugin authority hybrid (path-jail upstream of scanner)](../../clarion/adr/ADR-021-plugin-authority-hybrid.md) +- [ADR-023 — Tooling baseline (CI floor every PR must clear)](../../clarion/adr/ADR-023-tooling-baseline.md) +- [Requirements — NFR-SEC-01, NFR-SEC-04, NFR-OPS-01, NFR-OPS-04](../../clarion/v0.1/requirements.md) +- [System design — §10 Security, pre-ingest redaction paragraph](../../clarion/v0.1/system-design.md) +- [v0.1-plan.md — WP5 scope](../v0.1-plan.md#wp5--pre-ingest-secret-scanner) +- [Sprint-2 scope amendment — explicit WP5 deferral rationale, "production deployment against unknown corpora gates on this returning"](../sprint-2/scope-amendment-2026-05.md) +- [Arch analysis final report — §7 follow-ups #9 (L-1) and §5.3 L-2 (closed)](../../arch-analysis-2026-05-18-1244/04-final-report.md) diff --git a/docs/operator/README.md b/docs/operator/README.md index 2de58376..225676df 100644 --- a/docs/operator/README.md +++ b/docs/operator/README.md @@ -4,3 +4,5 @@ Practical notes for configuring and running Clarion. - [OpenRouter LLM provider](./openrouter.md) — API key, model ID, attribution headers, and token-ceiling configuration for v0.1. +- [Runtime topology](./runtime-topology.md) — supported `clarion serve` and + `clarion analyze` concurrency against one `.clarion/clarion.db`. diff --git a/docs/operator/clustering.md b/docs/operator/clustering.md new file mode 100644 index 00000000..a63d03bf --- /dev/null +++ b/docs/operator/clustering.md @@ -0,0 +1,101 @@ +# Clustering Operator Notes + +Clarion Phase 3 runs after plugin entity and edge extraction. It reads the +persisted module dependency graph, clusters modules, and writes subsystem +entities plus `in_subsystem` edges back into `.clarion/clarion.db`. + +## Configuration + +`clarion analyze` snapshots the resolved config into `runs.config`. + +```yaml +analysis: + clustering: + enabled: true + algorithm: leiden + seed: 42 + resolution: 1.0 + max_iterations: 100 + min_cluster_size: 3 + edge_types: [imports, calls] + weight_by: reference_count + weak_modularity_threshold: 0.3 +``` + +Supported algorithms are `leiden` and `weighted_components`. The +`weighted_components` fallback builds connected components over edges whose +weight is at least the graph's average positive edge weight; it is deterministic +and does not perform Louvain modularity optimisation. `edge_types` may include +`imports`, `calls`, or both. `weight_by` is currently `reference_count`. + +When `algorithm: leiden` produces zero or one community, Clarion computes the +local `weighted_components` fallback and uses it only if it produces more +communities than Leiden. Stored subsystem properties and +`runs.stats.clustering.algorithm` record the algorithm actually used, while +`runs.stats.clustering.configured_algorithm` keeps the requested config value. +So a run configured as `leiden` can report `weighted_components` when this +fallback fires. + +## Stored Subsystems + +Each emitted subsystem is an entity: + +- `id`: `core:subsystem:{cluster_hash}` +- `plugin_id`: `core` +- `kind`: `subsystem` +- `properties`: algorithm, seed, resolution, max iterations, modularity score, + cluster hash, member module IDs, member count, edge types, and weight mode + +Every member module has an `in_subsystem` edge pointing to the subsystem: + +```sql +SELECT from_id AS module_id, to_id AS subsystem_id +FROM edges +WHERE kind = 'in_subsystem'; +``` + +## MCP Access + +Use `subsystem_members` to inspect the modules assigned to a subsystem: + +```json +{ + "name": "subsystem_members", + "arguments": { + "id": "core:subsystem:abc123def456" + } +} +``` + +The response includes subsystem properties and ordered member modules. Calling +`summary` on a subsystem returns `available=false` with reason +`summary-scope-deferred`; subsystem summarization is deferred to v0.2 and does +not call the LLM provider in v0.1. + +## Weak Modularity + +Clarion emits a fact finding with rule +`CLA-FACT-CLUSTERING-WEAK-MODULARITY` when clustering succeeds but the +modularity score is below `analysis.clustering.weak_modularity_threshold` +(default `0.3`; set `0.0` to disable the finding). This means the graph did not +separate cleanly into strong communities. Treat it as operator guidance, not a +defect: inspect the subsystem membership, then decide whether the project needs +different config, graph pruning, or an ADR amendment. + +## Empty Inputs + +If no module dependency edges exist, Clarion emits no subsystems and records: + +```json +{ + "clustering": { + "status": "skipped", + "skipped_reason": "no_module_dependency_edges", + "subsystem_count": 0 + } +} +``` + +Single-module or too-small clusters similarly produce no subsystem rows when +they do not satisfy `min_cluster_size`; check `runs.stats.clustering` for the +exact skip reason. diff --git a/docs/operator/openrouter.md b/docs/operator/openrouter.md index f4349c58..f518b5e3 100644 --- a/docs/operator/openrouter.md +++ b/docs/operator/openrouter.md @@ -67,6 +67,17 @@ reached, MCP responses use: - diagnostic: `CLA-LLM-TOKEN-CEILING-EXCEEDED` - stat: `token_ceiling_exceeded_total` +The ceiling is scoped to the running `clarion serve` process. Once a live LLM +call attempts to exceed `llm_policy.session_token_ceiling`, Clarion blocks new +cold LLM dispatches for the rest of that process lifetime. Cache hits can still +be returned while the budget is blocked, because they do not spend additional +tokens. + +To clear a blocked LLM budget, stop and restart `clarion serve`. To change the +future ceiling, edit `llm_policy.session_token_ceiling` in `clarion.yaml` before +restarting. Clarion v0.1 intentionally has no MCP tool that resets the in-memory +budget ledger. + Dollar budgeting remains an operator concern in OpenRouter billing controls. ## CI And Replay diff --git a/docs/operator/runtime-topology.md b/docs/operator/runtime-topology.md new file mode 100644 index 00000000..1302d617 --- /dev/null +++ b/docs/operator/runtime-topology.md @@ -0,0 +1,59 @@ +# Runtime Topology + +Clarion stores project state in `.clarion/clarion.db`. The current v0.1 CLI +uses SQLite WAL mode with a 5 second `busy_timeout` on writer and reader +connections. `clarion analyze` opens one writer actor for ingest. `clarion +serve` always opens a reader pool, and opens its own writer actor only when LLM +summary or inferred-edge writes are enabled by `clarion.yaml`. + +These storage settings are implementation constants today, not configurable +`clarion.yaml` keys: + +- write connections set `journal_mode=WAL`, `synchronous=NORMAL`, + `busy_timeout=5000`, `wal_autocheckpoint=1000`, and `foreign_keys=ON` +- read connections set `busy_timeout=5000` and `foreign_keys=ON` +- analyze and serve writer actors each use a bounded command queue of 256 + operations + +## Supported + +One `clarion analyze` process and one `clarion serve` process may run against +the same `.clarion/clarion.db`. `serve` reads use committed SQLite snapshots: +in-flight analyze writes are invisible until their transaction commits and a +later read checks out a connection. If LLM-backed `serve` writes race with +analyze ingest, SQLite serialises the writers and waits up to 5 seconds before +returning a lock error. + +This topology is the default local workflow: + +```sh +clarion analyze . +clarion serve --path . +``` + +Long analyze runs can make `serve` responses stale relative to the source tree +until the relevant analyze batches commit. For the least surprising results, +start `serve` after a completed analyze run when operators need a stable +snapshot for a review session. + +## Unsupported + +Do not run multiple `clarion analyze` processes against the same +`.clarion/clarion.db`. Clarion has one writer actor per process, not one global +writer across processes, so two analyze runs can contend at SQLite's single +writer boundary and produce interleaved run state. + +Do not run `clarion install --force` while either `clarion analyze` or +`clarion serve` is using the same project. `--force` replaces `.clarion/`, so it +is an offline maintenance operation. + +Do not delete SQLite sidecar files, copy `.clarion/clarion.db` without its WAL +sidecars, or edit `.clarion/` files while Clarion is running. Stop the processes +first, then copy or repair the store. + +## Not Yet Shipped + +ADR-011 describes a future shadow database mode for zero-stale reads during +long analysis runs. The current CLI does not expose a `--shadow-db` flag, so +operators should treat in-place analyze plus WAL as the only shipped v0.1 +runtime topology. diff --git a/docs/superpowers/handoffs/2026-05-03-skeleton-audit.md b/docs/superpowers/handoffs/2026-05-03-skeleton-audit.md index 45774ad2..5824b46a 100644 --- a/docs/superpowers/handoffs/2026-05-03-skeleton-audit.md +++ b/docs/superpowers/handoffs/2026-05-03-skeleton-audit.md @@ -407,6 +407,8 @@ naming and split doctrine vs. schema fix) shaped Phase 2. F-1 through F-8 are absorbed by ADR-024 (`docs/clarion/adr/ADR-024-guidance-schema-vocabulary.md`) and the Phase 1 + Phase 2 commits on this branch. The original priority-affinity bug `clarion-4cd11905e2` is closed with the audit-resolution comment. +F-13 is absorbed by [ADR-031](../../clarion/adr/ADR-031-schema-validation-policy.md) (2026-05-18): CHECK constraints on closed core-owned vocabularies (`findings.{kind,severity,status}`, `runs.status`); writer-actor + ADR-022 manifest acceptance remain the only enforcement layer for plugin-extensible vocabularies (`entities.kind`, `edges.kind`). Filigree issue `clarion-fbe50aa6e1` closed. + ### Naming refinements applied to Phase 2 The original audit proposed `composition_level`/`composition_rank`, diff --git a/docs/superpowers/handoffs/2026-05-18-phase3-subsystems-handoff.md b/docs/superpowers/handoffs/2026-05-18-phase3-subsystems-handoff.md new file mode 100644 index 00000000..9e08c35a --- /dev/null +++ b/docs/superpowers/handoffs/2026-05-18-phase3-subsystems-handoff.md @@ -0,0 +1,186 @@ +# Handoff — Phase 3 Subsystems (analyse + implement) + +**Date**: 2026-05-18 +**For**: an agent picking this up cold +**Predecessor context**: Sprint 2 closed GREEN; [arch-analysis 2026-05-18](../../arch-analysis-2026-05-18-1244/04-final-report.md) is the current-state snapshot; [Thread-1 publish-prep program](../../implementation/v0.1-publish/thread-1-pre-publish-blockers.md) runs in parallel to this and does not block. + +--- + +## Why you were dispatched + +The amended-v0.1 MCP-MVP delivers entity extraction + on-demand leaf summarisation, but the *headline capability* the v0.1 requirements promise — **subsystems as first-class entities derived from clustering** — is missing. `REQ-CATALOG-05` (subsystem entities), `REQ-ANALYZE-01`/`REQ-ANALYZE-05` (Phase 3 in the pipeline), and `ADR-006` plus `ADR-032` (Leiden / weighted-components on imports+calls) collectively specify this. Nothing in the storage schema, the analyze orchestrator, or the MCP surface ships it yet. An agent asking "what is the auth subsystem of this codebase" currently gets back individual function entities; the aggregation level above the module does not exist. + +Closing this gap is the single highest-leverage move between the current MCP-MVP and the briefing's core pitch. + +## What you are delivering + +Two things, in order, with a human review gate between them. + +1. **An implementation plan** (file: `docs/superpowers/plans/2026-XX-XX-phase3-subsystems.md`) in the existing plan-doc convention (see [`docs/superpowers/plans/2026-05-05-b2-class-module-entities.md`](../plans/2026-05-05-b2-class-module-entities.md) for the canonical shape). Task-by-task, file-by-file, with exit criteria each task. +2. **The implementation itself**, executed task-by-task under TDD discipline, after the human approves the plan. + +**Do not skip Phase 1.** Phase 3 clustering touches the schema, the analyze orchestrator, the MCP read surface, and (when WP6 module/subsystem aggregation lands in v0.2) the LLM pipeline. The plan is the surface where the human catches "you missed `runs.stats` serialisation" or "the `in_subsystem` edge needs the writer-actor's edge-contract validator updated" before you write the wrong code for an afternoon. + +## Required sub-skills + +- `superpowers:brainstorming` — REQUIRED for Phase 1. Phase 3 is not a mechanical translation; there are real design judgments (Leiden source: vendored vs crate; Phase 3 placement in the analyze lifecycle; what `in_subsystem` looks like in the existing edge ontology; what to do when clustering input is empty). Brainstorm before drafting. +- `superpowers:writing-plans` — for the plan doc itself. +- `superpowers:subagent-driven-development` or `superpowers:executing-plans` — for Phase 2 implementation. +- `superpowers:test-driven-development` — RIGID, not optional. The arch-analysis flagged `analyze::run`'s `SoftFailed` branch as the canonical cautionary tale about adding code paths without tests; the H-1 fix (`clarion-141ca7de30`) covered exactly this. Do not extend the analyze orchestrator without a test that exercises the new path. +- `superpowers:verification-before-completion` — before any "done" claim, run the full ADR-023 floor (fmt / clippy `-D warnings` / nextest / doc-D / deny / ruff / mypy / pytest) and the walking-skeleton E2E. + +## Required reading (in this order) + +1. **`docs/clarion/adr/ADR-006-clustering-algorithm.md` plus ADR-032** — the authoritative spec. Read in full. Leiden on directed weighted imports+calls subgraph, seeded for determinism, with `weighted_components` as the named local fallback after ADR-032. Output is one `subsystem` entity per cluster + `in_subsystem` edges from members. Modularity reported, not enforced. +2. **`docs/clarion/adr/ADR-022-core-plugin-ontology.md`** — `subsystem` is a core-reserved entity kind; `in_subsystem` is a core-reserved edge kind. Plugins cannot emit either. The writer-actor's edge-contract validator already knows about plugin-extensible vs core-reserved (`writer.rs:411` per arch-analysis). +3. **`docs/clarion/adr/ADR-003-entity-id-scheme.md`** — subsystem IDs follow `core:subsystem:{cluster_hash}` per ADR-006 §Output. The hash is `sha256(sorted(member_module_ids))` truncated to 12 chars; verify the existing entity-ID validator accepts this shape (it should — `core` is a registered plugin_id per ADR-022). +4. **`docs/clarion/v0.1/requirements.md`** — REQ-CATALOG-05 (subsystem entities), REQ-ANALYZE-01 (phased pipeline), REQ-ANALYZE-05 (Phase-7 findings — relevant because `CLA-FACT-CLUSTERING-WEAK-MODULARITY` is named in ADR-006 §Quality assessment). +5. **`docs/clarion/v0.1/system-design.md` §6** — pipeline phases. Phase 3 placement, what it reads from storage, what it writes. +6. **`docs/clarion/v0.1/detailed-design.md`** — search for `subsystem`, `cluster`, `Phase 3`. Schema shape if present, properties expected on the subsystem entity. +7. **Current code surface** — `cargo` over these files at minimum: + - `crates/clarion-storage/migrations/0001_initial_schema.sql` — does `entities.kind` already accept `subsystem`? Does `edges.kind` accept `in_subsystem`? ADR-031 added CHECK constraints on closed vocabularies; verify the subsystem path is not constrained-shut. + - `crates/clarion-storage/src/writer.rs` (around line 394–411) — `STRUCTURAL_EDGE_KINDS` and `ANCHORED_EDGE_KINDS` registers. Arch-analysis H-2 noted these duplicate the manifest's edge-kind list (now closed as `clarion-4e3cacac90`); confirm what the closure shipped. + - `crates/clarion-storage/src/query.rs` — what helpers exist for module-level edge enumeration? + - `crates/clarion-cli/src/analyze.rs` — where Phase 1 (entity ingest) and Phase 2 (graph completion if implemented) currently end. Find the seam Phase 3 plugs into. Note that the file is `#[allow(clippy::too_many_lines)]` and arch-analysis flagged it (H-1 closed); if you add to it, factor cleanly. + - `crates/clarion-mcp/src/lib.rs` — the 7 MCP tools. Specifically `neighborhood`, `find_entity`, `execution_paths_from` — these will become more useful with subsystems but may need shape changes. **Do not change MCP tool surfaces silently.** Surface every proposed change in the plan. +8. **`docs/implementation/sprint-2/scope-amendment-2026-05.md`** — what was explicitly deferred. WP4 Phase 3 was deferred *with this work in mind*; you are pulling it forward from v0.2 to closing-of-v0.1. +9. **`docs/arch-analysis-2026-05-18-1244/02-subsystem-catalog.md`** — current code geography. The `clarion-storage` and `clarion-cli` entries describe the writer-actor, query helpers, and analyze orchestrator in concrete terms. + +## Scope discipline — what's IN and what's OUT + +**In scope (deliver):** +- Phase 3 clustering as a new step in `analyze::run`, after structural entity/edge ingest, before run commit. +- Leiden-default clustering over the (`imports` ∪ `calls`) module-level subgraph, weighted by `reference_count`, seeded from `clarion.yaml`, deterministic. +- Weighted-components as a config-selectable fallback (`analysis.clustering.algorithm: weighted_components`). +- Emit one `core:subsystem:{cluster_hash}` entity per cluster ≥ `min_cluster_size` (default 3). Properties per ADR-006 §Output. +- Emit `in_subsystem` edges from each member module to its subsystem entity. Edge ontology updated where required. +- New `clarion.yaml` keys under `analysis.clustering` (algorithm / seed / resolution / min_cluster_size / edge_types / weight_by). Defaults match ADR-006. +- Persist `modularity_score` and the algorithm/seed/resolution to the subsystem entity's properties **and** to `runs.stats` for the run-level record. +- Emit `CLA-FACT-CLUSTERING-WEAK-MODULARITY` (severity INFO) when overall modularity < 0.3, per ADR-006 §Quality assessment. (This is the only Phase-7 finding in scope here — the wider `CLA-*` catalogue remains v0.2.) +- A new MCP tool `subsystem_members(id)` (or extension of existing `neighborhood` to recognise `core:subsystem:*` entities — design choice; raise it in the plan). +- E2E test: a multi-module Python fixture clusters into at least 2 subsystems with the expected memberships. +- Determinism test: two consecutive runs against the same fixture produce byte-identical subsystem IDs and modularity scores. +- Documentation: a one-page `docs/operator/clustering.md` covering the config knobs and how to read the resulting subsystem entities. + +**Explicitly OUT of scope (do NOT do):** +- Subsystem *summarisation* (Phase 6 module/subsystem aggregation). ADR-030 defers this to v0.2; do not invoke the LLM on subsystem entities. `summary(id)` on a `core:subsystem:*` entity should return the existing leaf-summary-not-available envelope shape until v0.2. +- The full Phase-7 `CLA-*` cross-cutting rule catalogue. Only the one weak-modularity finding above. +- Catalog artefacts (`catalog.json` + per-subsystem markdown) — REQ-ARTEFACT-01/02 are deferred and have no MVP consumer. +- Multi-language plugin support — `imports` and `calls` are Python-plugin emissions for v0.1. Cross-language subsystems are NG-15. +- Schema-breaking migrations. ADR-024 still allows edit-in-place; verify that's the right policy here (it should be — no external operator has built `.clarion/clarion.db` from a published Clarion yet) and call it out explicitly in the plan. +- HTTP read API exposure. The HTTP read API is itself unimplemented; surfacing subsystems through it is v0.2. + +## Phase 1 — Analysis (your first job) + +Produce `docs/superpowers/plans/2026-XX-XX-phase3-subsystems.md` answering, at minimum: + +### A. Current-state audit + +Read the code; do not trust the ADRs as a description of the *current* implementation. Answer: + +1. Does `entities.kind` currently accept `subsystem`? Does `edges.kind` accept `in_subsystem`? Cite the migration line numbers. +2. Where in `analyze::run` does structural ingest end and run-commit begin? Cite the line range. +3. Does the writer-actor have a path for emitting a subsystem entity (no plugin source)? Or do you need a new `WriterCmd` variant (`InsertCoreEntity` / `InsertSubsystem`)? +4. What module-level edge data exists post-Phase-1? (Calls are emitted at function-level per B.4*; you need to aggregate them to module-level — confirm this isn't already done.) +5. What does the existing entity-ID validator (`clarion-core::entity_id`) say about `core:subsystem:abc123def456`? Run the fixtures. + +### B. Open design decisions to surface + +Each gets a recommendation + the alternatives + the reason for the recommendation: + +1. **Leiden source.** Vendor (~400 LOC per ADR-006) or adopt a maintained crate. Check `crates.io` at planning time. ADR-006 explicitly leaves this open. +2. **`in_subsystem` edge placement.** Is it `structural` or `anchored` in the existing edge ontology? Does it appear in `STRUCTURAL_EDGE_KINDS`? Does the manifest need to declare it (no — core-owned per ADR-022)? +3. **`subsystem_members` MCP tool vs extending `neighborhood`.** Both work. Which keeps the tool catalogue cleaner? +4. **Empty-input handling.** When the imports+calls subgraph is empty (single-module fixture, or analysis fails Phase 1), what does Phase 3 do? Skip silently? Emit zero subsystems and a `CLA-FACT-CLUSTERING-NO-INPUT` finding? Recommend. +5. **`runs.stats` shape.** The existing `runs.stats` is a JSON blob. Where does the modularity score sit in it? Define the JSON shape additively. +6. **Migration policy.** Does this need a new migration, or does ADR-024 edit-in-place still apply? Justify. + +### C. File map + +A table of every file you will create / modify, with the task that touches it. Same shape as the B.2 plan's file map. + +### D. Task breakdown + +5–8 tasks, each sized to ≤500 LOC + tests, each with: scope, files, tests, exit. Sequenced. + +### E. Exit criteria for the whole workstream + +- ADR-023 floor green. +- E2E test on the multi-module fixture green. +- Determinism test green. +- The Sprint-1 walking-skeleton E2E continues to pass (no regression on the single-file fixture). +- The MCP `summary` tool on a subsystem entity returns the policy envelope (not a budget-consuming LLM call). +- `clarion analyze` against the existing elspeth-slice perf harness still completes within the NFR-PERF-01 envelope; if Phase 3 adds noticeable cost, the plan must include a measurement step. + +### F. Risks and unknowns + +Name them. The week-2 go/no-go gate concept from B.4* (`docs/implementation/sprint-2/scope-amendment-2026-05.md` §5) is worth borrowing — define a measurable "Leiden over elspeth-slice's module subgraph runs in < N seconds" gate halfway through implementation. If it fails, the weighted-components fallback is the documented response. + +## Review gate + +**Stop after Phase 1.** Write the plan, commit it, and surface it to the human. Do not start implementation until the human approves the plan in writing (either a Filigree comment or a direct message). The plan-review skill (`axiom-planning:plan-review`) is available if the human wants a structured second-opinion pass before approving. + +## Phase 2 — Implementation + +Execute the plan task-by-task under TDD. For each task: + +1. Write the failing test first. +2. Make it pass with the smallest change that compiles and clippies cleanly. +3. Run the ADR-023 floor locally before declaring the task complete. +4. Mark the task complete in the plan file (`- [x]`) and commit; one commit per task with a message that names the task and cites the relevant ADR/REQ ID. + +**Do not** batch multiple tasks into a single commit. The plan's checkbox shape exists so a reviewer can read the commit log against the plan and verify task-by-task. Sprint 2's B.4* + B.6 commit ranges followed this discipline; mimic them. + +**Do not** silently change MCP tool surfaces. If during implementation you discover the `neighborhood` tool needs a shape tweak you didn't predict, stop and surface it — update the plan, commit the plan update, then resume. + +## Filigree workflow + +Before starting Phase 1: + +```bash +filigree create --type=work_package --title="WP4 Phase 3 — Subsystem clustering (REQ-CATALOG-05, ADR-006)" \ + --labels="release:v0.1,sprint:3,wp:4,adr:006,tier:a" --priority=P1 +# Capture the new issue ID; this is the umbrella. + +filigree start-work --assignee +``` + +Then, when the plan is committed and approved, create per-task issues blocked-by the umbrella so an outside reader of the Filigree dashboard can see exactly what's being worked. + +When Phase 2 finishes: + +```bash +filigree close --reason="Phase 3 clustering shipped; subsystem entities live; ADR-006 satisfied" +``` + +## Authorities and overrides + +- **ADR-006 is authoritative on algorithm.** If your implementation reveals the ADR is wrong (e.g., directed-modularity Leiden produces nonsense on some pattern of the elspeth graph), do NOT silently switch. Stop, document the empirical finding, and propose an ADR amendment. ADRs are immutable once Accepted (`CLAUDE.md` editorial conventions); the right response is a new ADR that supersedes, not a silent code-level change. +- **The Loom federation axiom (`docs/suite/loom.md` §5)** is load-bearing. Phase 3 is internal to Clarion and does not touch sibling products, so this should not bite. If you find yourself proposing a cross-product change, you've gone out of scope. +- **The tooling baseline (ADR-023)** is non-negotiable per PR. If a clippy lint blocks you, fix the lint; do not `#[allow]` it without writing the justification into the code and the plan. + +## Done condition + +This handoff is satisfied when: + +- The plan exists at `docs/superpowers/plans/2026-XX-XX-phase3-subsystems.md`, approved by the human. +- All plan tasks are checked off and committed. +- The Filigree umbrella is `closed` with a close reason that names the merge commits. +- The walking-skeleton E2E + a new subsystems E2E + the determinism test are all green in CI. +- A subsequent `clarion analyze && clarion serve` on a multi-module fixture lets a consult-mode agent ask "what are the subsystems of this project" and get back a non-empty, sensibly-named list of subsystem entities. + +The last bullet is the actual capability the work delivers. If it works in CI but a real agent session against a real fixture doesn't surface meaningful subsystems, you haven't shipped the feature. + +## References + +- [ADR-006 — Clustering algorithm](../../clarion/adr/ADR-006-clustering-algorithm.md) +- [ADR-022 — Core/plugin ontology](../../clarion/adr/ADR-022-core-plugin-ontology.md) +- [ADR-003 — Entity-ID scheme](../../clarion/adr/ADR-003-entity-id-scheme.md) +- [ADR-024 — Migration edit-in-place policy](../../clarion/adr/ADR-024-guidance-schema-vocabulary.md) +- [ADR-031 — Schema validation policy (CHECK constraints)](../../clarion/adr/ADR-031-schema-validation-policy.md) +- [REQ-CATALOG-05, REQ-ANALYZE-01, REQ-ANALYZE-05](../../clarion/v0.1/requirements.md) +- [v0.1-plan.md WP4](../../implementation/v0.1-plan.md#wp4--core-only-pipeline-phases-03-7-8) +- [Sprint-2 scope amendment — explicit Phase 3 deferral with retirement path](../../implementation/sprint-2/scope-amendment-2026-05.md) +- [Arch-analysis 2026-05-18 — current code geography](../../arch-analysis-2026-05-18-1244/04-final-report.md) +- [B.2 plan-doc shape — canonical example](../plans/2026-05-05-b2-class-module-entities.md) +- [Sprint-2 B.4* — the week-2 go/no-go gate pattern to mimic](../../implementation/sprint-2/scope-amendment-2026-05.md#5-the-week-2-gono-go-gate-load-bearing-risk) diff --git a/docs/superpowers/plans/2026-05-18-phase3-subsystems.md b/docs/superpowers/plans/2026-05-18-phase3-subsystems.md new file mode 100644 index 00000000..ce04fb7d --- /dev/null +++ b/docs/superpowers/plans/2026-05-18-phase3-subsystems.md @@ -0,0 +1,729 @@ +# Phase 3 Subsystems - Implementation Plan + +> **For agentic workers:** REQUIRED SUB-SKILLS for implementation: use +> `superpowers:executing-plans` or `superpowers:subagent-driven-development`, +> then use `superpowers:test-driven-development` and +> `superpowers:verification-before-completion` for every task. This plan is +> the Phase 1 review artifact; do not start implementation until the human +> approves it in writing. + +**Goal:** Add WP4 Phase 3 subsystem clustering to `clarion analyze`, satisfying +`REQ-CATALOG-05`, `REQ-ANALYZE-01`, and ADR-006: module-level clustering over +`imports` plus `calls`, one `core:subsystem:{cluster_hash}` entity per cluster, +`in_subsystem` edges from member modules, run stats, the weak-modularity fact, +MCP membership lookup, determinism coverage, and operator documentation. + +**Architecture:** `clarion analyze` remains the single write path. Phase 3 plugs +in after plugin entities/edges are inserted and before `CommitRun`. Storage +gets read helpers that aggregate module-level dependency edges from the +persisted graph. A new CLI-side clustering module turns that graph into +subsystem entity/edge write commands. MCP reads the resulting graph; it does +not run clustering itself. + +**Tech Stack:** Rust 2024 workspace, rusqlite, serde/serde_json, +serde_norway, sha2 for ADR-006 subsystem hashes, a graph-clustering crate +candidate qualified in Task 1, Python 3.11 AST extraction for import edges, +pytest, mypy, ruff, cargo nextest, cargo-deny, and existing shell E2E scripts. + +**Spec:** ADR-006, ADR-003, ADR-022, `docs/clarion/v0.1/requirements.md`, +`docs/clarion/v0.1/system-design.md`, and the Phase 3 handoff +`docs/superpowers/handoffs/2026-05-18-phase3-subsystems-handoff.md`. + +**Filigree umbrella:** `clarion-1dfeebfa36` (P1 work_package; +`release:v0.1`, `sprint:3`, `wp:4`, `adr:006`, `tier:a`). Current status: +`executing`, assigned to `codex`. + +--- + +## Current-State Audit + +1. **Schema accepts subsystem and in_subsystem without a new migration.** + `entities.kind` is plugin-extensible and has no CHECK constraint + (`crates/clarion-storage/migrations/0001_initial_schema.sql:30-37`). + `edges.kind` is also plugin-extensible with writer-side enforcement rather + than a CHECK (`:80-85`). The migration header still documents the ADR-024 + edit-in-place policy and the 2026-05-18 CHECK edits (`:1-16`). The existing + schema can store `subsystem` entities and `in_subsystem` edges. + +2. **Structural ingest ends in `analyze::run` after plugin edges are inserted.** + The per-plugin loop collects accepted entities, edges, unresolved sites, and + stats (`crates/clarion-cli/src/analyze.rs:216-405`). Entities are inserted + before unresolved sites, then edges, so edge foreign keys resolve at insert + time (`:322-396`). Run-commit outcome handling begins immediately after the + plugin loop (`:407-424`). Phase 3 belongs between those two blocks. + +3. **Subsystem entities can use the existing writer path.** `EntityRecord` + already supports `source_* = None`, `content_hash = None`, and arbitrary + `properties_json` (`crates/clarion-storage/src/commands.rs:48-70`), and + `WriterCmd::InsertEntity` is generic (`:112-174`). `writer.rs` inserts the + generic record after `BeginRun` (`crates/clarion-storage/src/writer.rs:332-385`). + No `InsertSubsystem` command is required. A new `InsertFinding` command is + required for the weak-modularity fact because findings currently have a + table but no writer command. + +4. **Module-level dependency data is incomplete today.** Module entities and + `contains` parent edges exist. `calls` and `references` are emitted at + function/entity level. There is no storage helper that aggregates those + edges to module-to-module dependencies (`crates/clarion-storage/src/query.rs` + currently has call, reference, and contains helpers but no subsystem graph + helper). The Python plugin manifest declares `contains`, `calls`, and + `references` only (`plugins/python/plugin.toml:31-46`), and the extractor + docs still say import emission is future scope + (`plugins/python/src/clarion_plugin_python/extractor.py:1-44`). Phase 3 + therefore needs Python `imports` edge emission plus a storage aggregation + helper for both `imports` and function-level `calls`. + +5. **Entity ID shape is already valid.** `clarion_core::entity_id` accepts + `plugin_id = "core"`, `kind = "subsystem"`, and a 12-hex canonical name; + an existing unit test already covers `core:subsystem:a1b2c3d4` + (`crates/clarion-core/src/entity_id.rs:90-105`, `:192-194`). Verification + run during planning: + + ```bash + cargo test -p clarion-core core_reserved_subsystem_kind -- --nocapture + cargo test -p clarion-core shared_ -- --nocapture + plugins/python/.venv/bin/pytest \ + plugins/python/tests/test_entity_id.py::test_matches_shared_fixture \ + plugins/python/tests/test_entity_id.py::test_matches_shared_contains_edge_fixture \ + plugins/python/tests/test_entity_id.py::test_matches_shared_calls_edge_fixture -q + ``` + + Results: all selected tests passed. + +--- + +## Design Decisions + +### 1. Leiden source + +**Recommendation:** adopt a maintained crate for the default Leiden pass, with +a small adapter layer and a dependency-qualification gate in Task 1. The first +candidate is `xgraph` because current docs explicitly advertise directed and +undirected graph support, deterministic/randomized execution, seed support, +and modularity-oriented Leiden clustering. Post-landing ADR-032 names the local +fallback `weighted_components` because the implementation is deterministic BFS +over high-weight edges, not Louvain modularity optimisation. + +Planning-time crate check, 2026-05-18: + +- `xgraph` docs: directed/undirected graph algorithms, Leiden clustering, + deterministic mode, and `seed` in `CommunityConfig` + (https://docs.rs/xgraph/latest/xgraph/ and + https://docs.rs/xgraph/latest/src/xgraph/graph/algorithms/leiden_clustering.rs.html). +- `leiden-rs` docs: maintained Leiden implementation, modularity quality + functions, and a `from_gryf_directed` adapter, but the docs snippet did not + establish a seeded deterministic API clearly enough for ADR-006 on its own + (https://docs.rs/leiden-rs/latest/leiden_rs/). +- `single-clustering` docs: Leiden, Louvain, `seed: Some(42)`, and modularity, + but Louvain is documented as work-in-progress and directed graph semantics + were not explicit (https://docs.rs/crate/single-clustering/0.6.1). +- `sdivi_detection` docs: deterministic native Leiden with modularity/CPM, but + no Louvain fallback surface was evident in the docs + (https://docs.rs/sdivi-detection/latest/sdivi_detection/). + +Task 1 is a hard gate: if the chosen crate fails cargo-deny, does not compile +on the pinned Rust toolchain, or cannot preserve directed weighted semantics +with a fixed seed in tests, stop and amend this plan before Task 2. + +### 2. in_subsystem edge placement + +**Recommendation:** keep `in_subsystem` structural and core-owned. The writer +already lists it in `STRUCTURAL_EDGE_KINDS` +(`crates/clarion-storage/src/writer.rs:450-457`) and rejects source ranges on +structural edges (`:478-502`). The Python plugin must not declare or emit it; +the core clustering module emits it after the subsystem entity is inserted. + +Direction: `member_module -> subsystem`. The MCP membership helper queries +`edges.kind = 'in_subsystem' AND edges.to_id = subsystem_id`. + +### 3. MCP surface + +**Recommendation:** add a new `subsystem_members(id)` MCP tool rather than +folding the behavior into `neighborhood`. Requirements already name +`subsystem_members` (`docs/clarion/v0.1/requirements.md:365-371`), and a +separate tool keeps the response schema narrow: subsystem metadata plus an +ordered member list. `neighborhood` can later include subsystem links +additively, but that should not be the only way to inspect a subsystem. + +Also add a policy branch to `summary(id)` for `kind = 'subsystem'`: return the +existing non-LLM policy/error envelope before content-hash lookup or provider +dispatch. Subsystem summarization remains out of scope. + +### 4. Empty-input handling + +**Recommendation:** emit zero subsystems, no finding, and explicit run stats: + +```json +{ + "clustering": { + "enabled": true, + "algorithm": "leiden", + "status": "skipped", + "skipped_reason": "no_module_dependency_edges", + "module_count": 1, + "module_edge_count": 0, + "subsystem_count": 0, + "modularity_score": null + } +} +``` + +Do not create `CLA-FACT-CLUSTERING-NO-INPUT`; the handoff explicitly limits +Phase 7 scope to the weak-modularity finding. Single-module and no-plugin +fixtures should remain quiet but inspectable through `runs.stats`. + +### 5. runs.stats shape + +**Recommendation:** add a single additive `clustering` object inside the +existing JSON stats blob. Existing top-level counters stay untouched. + +Successful run example: + +```json +{ + "entities_inserted": 120, + "edges_inserted": 340, + "dropped_edges_total": 0, + "ambiguous_edges_total": 0, + "clustering": { + "enabled": true, + "algorithm": "leiden", + "status": "completed", + "seed": 42, + "resolution": 1.0, + "max_iterations": 100, + "min_cluster_size": 3, + "edge_types": ["imports", "calls"], + "weight_by": "reference_count", + "module_count": 18, + "module_edge_count": 44, + "subsystem_count": 3, + "modularity_score": 0.417321, + "duration_ms": 37, + "weak_modularity_finding_emitted": false, + "skipped_reason": null + } +} +``` + +Soft-failed runs that reach Phase 3 should include the same `clustering` +object. Hard failures before Phase 3 keep the existing failure stats. + +### 6. Migration policy + +**Recommendation:** no schema migration. Use ADR-024 edit-in-place only if a +test fixture needs an index or helper view added; the current implementation +should not need that. `entities.kind` and `edges.kind` are already open by +policy, and `findings.kind`/`severity` already accept `fact` and `INFO` +(`crates/clarion-storage/migrations/0001_initial_schema.sql:103-136`). + +### 7. Weak-modularity finding anchor + +**Recommendation:** persist `CLA-FACT-CLUSTERING-WEAK-MODULARITY` as a `fact` +with severity `INFO`, anchored to the largest emitted subsystem entity. Put all +subsystem IDs in `related_entities` and include `run_id`, `modularity_score`, +`threshold`, and `algorithm` in `properties`. + +Reason: the current findings schema requires `entity_id NOT NULL` +(`crates/clarion-storage/migrations/0001_initial_schema.sql:119`). Making +run-level findings nullable or inventing a `core:run:*` entity is a schema and +ontology change outside this handoff. If modularity is unavailable because +there are no emitted subsystems, record the skip reason in `runs.stats` and do +not emit a finding. + +--- + +## File Map + +| File | Role | Tasks | +|---|---|---| +| `Cargo.toml` | Add graph/hash dependencies after Task 1 qualification | 1 | +| `Cargo.lock` | Lock dependency graph | 1 | +| `crates/clarion-cli/src/main.rs` | Pass analyze config path into `analyze::run` | 2 | +| `crates/clarion-cli/src/cli.rs` | Add `clarion analyze --config ` | 2 | +| `crates/clarion-cli/src/config.rs` | New analyze config parser and defaults for `analysis.clustering` | 2 | +| `crates/clarion-cli/src/analyze.rs` | Accept config, persist config JSON, filter candidate `imports` before writer insertion, call Phase 3 before commit, merge clustering stats | 2, 3, 5 | +| `crates/clarion-cli/src/clustering.rs` | New Phase 3 graph/algorithm/subsystem writer orchestration | 1, 4, 5 | +| `crates/clarion-cli/Cargo.toml` | Wire dependencies used by config/clustering | 1, 2 | +| `crates/clarion-cli/tests/analyze.rs` | Config/run-stats/import-filter/Phase-3 integration tests | 2, 3, 5 | +| `plugins/python/plugin.toml` | Add `imports`; bump plugin and ontology versions | 3 | +| `plugins/python/src/clarion_plugin_python/__init__.py` | Bump package version | 3 | +| `plugins/python/src/clarion_plugin_python/server.py` | Bump ontology constant; pass import resolver inputs if needed | 3 | +| `plugins/python/src/clarion_plugin_python/extractor.py` | Extract AST import sites and emit candidate `imports` edges | 3 | +| `plugins/python/tests/test_extractor.py` | Import-edge unit coverage | 3 | +| `plugins/python/tests/test_round_trip.py` | Manifest/round-trip coverage for `imports` | 3 | +| `fixtures/entity_id.json` | Shared import-edge fixture rows if parity helpers grow | 3 | +| `crates/clarion-core/src/entity_id.rs` | Optional shared fixture parity for `imports` edge shape | 3 | +| `crates/clarion-storage/src/query.rs` | Module dependency graph and subsystem membership helpers | 4, 6 | +| `crates/clarion-storage/src/lib.rs` | Re-export new query structs/helpers if needed | 4, 6 | +| `crates/clarion-storage/src/commands.rs` | Add `FindingRecord` and `WriterCmd::InsertFinding` | 5 | +| `crates/clarion-storage/src/writer.rs` | Persist findings through writer actor | 5 | +| `crates/clarion-storage/tests/writer_actor.rs` | Finding writer and subsystem edge contract tests | 5 | +| `crates/clarion-storage/tests/schema_apply.rs` | Guard existing open vocabulary assumptions | 4, 5 | +| `crates/clarion-mcp/src/lib.rs` | Add `subsystem_members`; summary policy branch for subsystems | 6 | +| `crates/clarion-mcp/tests/storage_tools.rs` | MCP tool list, membership response, summary no-LLM tests | 6 | +| `tests/e2e/phase3_subsystems.sh` | New multi-module subsystem E2E and determinism check | 7 | +| `tests/e2e/sprint_1_walking_skeleton.sh` | Verify unchanged; only edit if necessary to keep current assertions honest | 7 | +| `tests/fixtures/phase3_subsystems/` | New multi-module Python fixture, if the E2E does not build it inline | 7 | +| `docs/operator/clustering.md` | One-page operator guide for clustering config/results | 7 | +| `docs/superpowers/plans/2026-05-18-phase3-subsystems.md` | Track task checkboxes during Phase 2 | 1-7 | + +--- + +## Task 1: Dependency Qualification and Algorithm Adapter Skeleton + +**Files:** +- Modify: `Cargo.toml` +- Modify: `Cargo.lock` +- Modify: `crates/clarion-cli/Cargo.toml` +- Add: `crates/clarion-cli/src/clustering.rs` +- Modify: `crates/clarion-cli/src/main.rs` only to `mod clustering;` + +**Scope:** Qualify the graph crate and create a tiny adapter boundary before +any analyze integration. This task does not write database rows. + +- [x] Write failing unit tests in `clustering.rs`: + - `fixed_seed_leiden_is_byte_stable` + - `directed_weighted_edges_affect_partition` + - `weighted_components_fallback_is_config_selectable` + - `cluster_hash_uses_sha256_sorted_member_ids_truncated_to_12` +- [x] Add `sha2 = "0.10"` and the selected graph crate to workspace deps. +- [x] Implement: + - `ClusterAlgorithm::{Leiden, WeightedComponents}` + - `ModuleGraph { modules, edges }` + - `ClusterConfig { algorithm, seed, resolution, max_iterations, min_cluster_size }` + - `ClusterResult { communities, modularity_score, algorithm_used }` + - `cluster_modules(&ModuleGraph, &ClusterConfig) -> anyhow::Result` + - `cluster_hash(member_ids: &[String]) -> String` +- [x] Run qualification gates: + +```bash +cargo test -p clarion-cli clustering -- --nocapture +cargo deny check +cargo tree -p clarion-cli +``` + +**Exit:** The tests prove fixed-seed determinism, directed weighted behavior, +config-selectable weighted-components fallback, and ADR-006 hash shape. `cargo deny check` passes +without broadening `deny.toml`. If not, stop and amend this plan. + +**Commit:** `feat(wp4): qualify clustering adapter (phase3 task 1)` + +--- + +## Task 2: Analyze Config Plumbing + +**Files:** +- Modify: `crates/clarion-cli/src/cli.rs` +- Modify: `crates/clarion-cli/src/main.rs` +- Add: `crates/clarion-cli/src/config.rs` +- Modify: `crates/clarion-cli/src/analyze.rs` +- Modify: `crates/clarion-cli/tests/analyze.rs` + +**Scope:** Give `clarion analyze` the `analysis.clustering` configuration +surface and persist the resolved config in `runs.config`. No subsystem rows yet. + +- [x] Write failing tests: + - `analyze_default_config_records_clustering_defaults` + - `analyze_config_file_overrides_clustering_seed_and_algorithm` + - `analyze_rejects_invalid_clustering_algorithm` +- [x] Add `AnalyzeConfig` with default: + +```yaml +analysis: + clustering: + enabled: true + algorithm: leiden + seed: 42 + resolution: 1.0 + max_iterations: 100 + min_cluster_size: 3 + edge_types: ["imports", "calls"] + weight_by: reference_count +``` + +- [x] Add `clarion analyze --config `, defaulting to + `/clarion.yaml` if present, otherwise defaults. +- [x] Change `analyze::run(path)` to accept an options/config value while + preserving tests that call the default path. +- [x] Replace the current `BeginRun.config_json = "{}"` with the resolved + analyze config JSON. + +**Exit:** Focused tests pass, invalid config fails before `BeginRun`, and +existing no-plugin/skipped tests still pass. + +```bash +cargo test -p clarion-cli analyze_default_config_records_clustering_defaults -- --nocapture +cargo test -p clarion-cli analyze_config_file_overrides_clustering_seed_and_algorithm -- --nocapture +cargo test -p clarion-cli analyze_rejects_invalid_clustering_algorithm -- --nocapture +cargo test -p clarion-cli analyze_without_plugins_writes_skipped_run_row -- --nocapture +``` + +**Commit:** `feat(wp4): add analyze clustering config (phase3 task 2)` + +--- + +## Task 3: Python imports Edge Emission + +**Files:** +- Modify: `crates/clarion-cli/src/analyze.rs` +- Modify: `crates/clarion-cli/tests/analyze.rs` +- Modify: `plugins/python/plugin.toml` +- Modify: `plugins/python/src/clarion_plugin_python/__init__.py` +- Modify: `plugins/python/src/clarion_plugin_python/server.py` +- Modify: `plugins/python/src/clarion_plugin_python/extractor.py` +- Modify: `plugins/python/tests/test_extractor.py` +- Modify: `plugins/python/tests/test_round_trip.py` +- Modify: `fixtures/entity_id.json` if shared parity is extended +- Modify: `crates/clarion-core/src/entity_id.rs` if shared parity is extended + +**Scope:** Emit anchored `imports` candidate edges from module entities. The +host filters candidate imports whose `to_id` module is not present in the same +analysis batch before writer insertion, so external imports do not trip edge +foreign keys. + +- [x] Write failing Python tests: + - `test_import_statement_emits_module_import_edge` + - `test_from_import_emits_import_edge_to_parent_module` + - `test_relative_import_emits_package_relative_module_edge` + - `test_import_edges_have_source_byte_range_and_resolved_confidence` +- [x] Write failing Rust host test: + - `analyze_filters_external_import_edges_before_writer_insert` +- [x] Add `ImportsEdgeProperties` with at least: + - `imported_name` + - `import_style` (`import` or `from_import`) + - `level` for relative imports +- [x] Add an AST import-site collector. Source range comes from the AST node's + byte offsets using the same source-buffer convention as calls/references. +- [x] Emit edges from current module entity to `python:module:{target}`. +- [x] In `run_plugin_blocking`, after all files in a plugin batch have been + analyzed and before returning `collected_edges` to the async writer-insert + path, filter `imports` edges to targets present in the batch's accepted + module entity IDs. Preserve internal imports; drop external or unresolved + imports with an additive `imports_skipped_external_total` counter in + `BatchStats`/`runs.stats` rather than allowing SQLite FK failure during + `WriterCmd::InsertEdge`. +- [x] Add `imports` to plugin manifest `edge_kinds`, bump ontology version and + package patch version. +- [x] Add or update shared edge parity fixture only if the current fixture + structure supports a fourth edge family cleanly. Not extended in this slice; + extractor and host-filter regressions cover the new edge family directly. + +**Exit:** Python unit tests, strict typing, linting, and round trip pass. The +walking skeleton still passes because a single file has no internal import +target after host filtering. + +```bash +plugins/python/.venv/bin/pytest plugins/python/tests/test_extractor.py -q +plugins/python/.venv/bin/pytest plugins/python/tests/test_round_trip.py -q +plugins/python/.venv/bin/mypy --strict plugins/python +plugins/python/.venv/bin/ruff check plugins/python +plugins/python/.venv/bin/ruff format --check plugins/python +cargo test -p clarion-cli analyze_filters_external_import_edges_before_writer_insert -- --nocapture +``` + +**Commit:** `feat(wp3): emit python imports edges (phase3 task 3)` + +--- + +## Task 4: Storage Query Helpers for the Module Graph + +**Files:** +- Modify: `crates/clarion-storage/src/query.rs` +- Modify: `crates/clarion-storage/src/lib.rs` +- Modify: `crates/clarion-storage/tests/schema_apply.rs` +- Add or modify storage query tests in the existing storage test suite + +**Scope:** Read the persisted graph into a module-level dependency graph, and +read subsystem memberships. No analyze integration yet. + +- [x] Write failing storage tests with seeded SQLite data: + - `module_dependency_edges_include_imports` + - `module_dependency_edges_roll_up_function_calls_to_parent_modules` + - `module_dependency_edges_weight_by_reference_count` + - `module_dependency_edges_skip_self_edges` + - `subsystem_members_returns_modules_ordered_by_name` +- [x] Add query structs: + +```rust +pub struct ModuleDependencyEdge { + pub from_module_id: String, + pub to_module_id: String, + pub reference_count: u64, + pub edge_kinds: Vec, +} + +pub struct SubsystemMember { + pub id: String, + pub name: String, + pub source_file_path: Option, +} +``` + +- [x] Implement: + - `module_dependency_edges(conn, edge_types) -> Result>` + - `subsystem_members(conn, subsystem_id) -> Result>` + - `subsystem_for_member(conn, module_id) -> Result>` +- [x] Preserve the existing rule that `imports` and `calls` are anchored edge + kinds, while `in_subsystem` is structural. + +**Exit:** Query tests pass and existing writer/schema tests still pass. + +```bash +cargo test -p clarion-storage module_dependency_edges -- --nocapture +cargo test -p clarion-storage subsystem_members -- --nocapture +cargo test -p clarion-storage schema_accepts_open_entity_and_edge_kinds -- --nocapture +``` + +**Commit:** `feat(storage): add subsystem graph queries (phase3 task 4)` + +--- + +## Task 5: Analyze Phase 3 Writes, Stats, and Weak-Modularity Finding + +**Files:** +- Modify: `crates/clarion-cli/src/analyze.rs` +- Modify: `crates/clarion-cli/src/clustering.rs` +- Modify: `crates/clarion-cli/tests/analyze.rs` +- Modify: `crates/clarion-storage/src/commands.rs` +- Modify: `crates/clarion-storage/src/writer.rs` +- Modify: `crates/clarion-storage/tests/writer_actor.rs` + +**Scope:** Insert subsystem entities and `in_subsystem` edges during +`clarion analyze`, then persist run-level clustering stats and the weak +modularity fact. + +- [x] Write failing Rust tests: + - `analyze_phase3_emits_subsystem_entities_and_edges` + - `analyze_phase3_is_deterministic_across_two_runs` + - `analyze_phase3_skips_empty_graph_with_stats` + - `analyze_phase3_emits_weak_modularity_fact_when_below_threshold` + - `writer_inserts_fact_findings` +- [x] Add `FindingRecord` and `WriterCmd::InsertFinding`. +- [x] Implement writer insertion for `findings`, including JSON fields as + serialized strings and `status = 'open'`. +- [x] Add `Phase3Output`: + - `subsystems_inserted` + - `in_subsystem_edges_inserted` + - `clustering_stats` + - `weak_modularity_finding` +- [x] In `analyze::run`, after plugin insertion and before outcome commit: + - read module dependency graph + - cluster if enabled + - insert subsystem entities + - insert `in_subsystem` edges + - insert weak-modularity finding if applicable + - merge clustering stats into completed or soft-failed stats JSON +- [x] Subsystem entity properties: + +```json +{ + "algorithm": "leiden", + "seed": 42, + "resolution": 1.0, + "max_iterations": 100, + "modularity_score": 0.417321, + "cluster_hash": "abc123def456", + "member_module_ids": ["python:module:a", "python:module:b"], + "member_count": 2, + "edge_types": ["imports", "calls"], + "weight_by": "reference_count" +} +``` + +**Exit:** Focused analyze/storage tests pass. Existing `ambiguous_edges_total` +and skipped/no-plugin stats tests still pass, proving stats additions are +additive. + +```bash +cargo test -p clarion-cli analyze_phase3 -- --nocapture +cargo test -p clarion-storage writer_inserts_fact_findings -- --nocapture +cargo test -p clarion-cli analyze_stats_reports_ambiguous_edges_total -- --nocapture +cargo test -p clarion-cli analyze_without_plugins_writes_skipped_run_row -- --nocapture +``` + +**Commit:** `feat(wp4): write subsystem clusters in analyze (phase3 task 5)` + +--- + +## Task 6: MCP subsystem_members and Subsystem Summary Policy + +**Files:** +- Modify: `crates/clarion-mcp/src/lib.rs` +- Modify: `crates/clarion-mcp/tests/storage_tools.rs` +- Modify: `crates/clarion-storage/src/query.rs` only if Task 4 helpers need + response-shape refinements + +**Scope:** Surface persisted subsystems through MCP without invoking the LLM. + +- [x] Write failing MCP tests: + - `tools_list_includes_subsystem_members` + - `subsystem_members_returns_member_modules` + - `subsystem_members_rejects_non_subsystem_id` + - `summary_on_subsystem_returns_policy_envelope_without_llm_call` +- [x] Add tool definition: + +```json +{ + "name": "subsystem_members", + "description": "List module entities assigned to a subsystem entity.", + "inputSchema": { + "type": "object", + "required": ["id"], + "properties": { + "id": { "type": "string" } + } + } +} +``` + +- [x] Response shape: + +```json +{ + "subsystem": { + "id": "core:subsystem:abc123def456", + "properties": { "member_count": 4, "modularity_score": 0.42 } + }, + "members": [ + { "id": "python:module:pkg.auth", "name": "pkg.auth", "source_file_path": "pkg/auth.py" } + ] +} +``` + +- [x] Add a `summary` early branch for subsystem kind that returns the + existing policy/error envelope and does not consult cache or provider. + +**Exit:** MCP tests pass and the existing seven tools are unchanged except for +the additive eighth tool. + +```bash +cargo test -p clarion-mcp subsystem_members -- --nocapture +cargo test -p clarion-mcp summary_on_subsystem_returns_policy_envelope_without_llm_call -- --nocapture +cargo test -p clarion-mcp tools_list -- --nocapture +``` + +**Commit:** `feat(mcp): expose subsystem membership tool (phase3 task 6)` + +--- + +## Task 7: E2E Fixture, Determinism Gate, Docs, and Performance Measurement + +**Files:** +- Add: `tests/e2e/phase3_subsystems.sh` +- Add: `tests/fixtures/phase3_subsystems/` if not generated inline +- Verify or modify: `tests/e2e/sprint_1_walking_skeleton.sh` +- Add: `docs/operator/clustering.md` +- Modify: `docs/superpowers/plans/2026-05-18-phase3-subsystems.md` + +**Scope:** Prove the user-facing workflow, document it, and run the performance +gate before declaring Phase 3 ready. + +- [x] Write a multi-module Python fixture with at least two dense internal + dependency groups and sparse cross-group edges. +- [x] Add E2E script: + - install project + - run `clarion analyze` + - assert at least two `subsystem` rows + - assert each subsystem has at least `min_cluster_size` module members + - assert `runs.stats.clustering.status = "completed"` + - run a second clean analysis and assert subsystem IDs and modularity match + - run `clarion serve` fixture interaction or a direct MCP harness call for + `subsystem_members` +- [x] Add `docs/operator/clustering.md` with: + - config keys and defaults + - what subsystem entities contain + - how to call `subsystem_members` + - what weak modularity means + - how empty/single-module input appears in stats +- [x] Performance gate: + - Use the existing elspeth-slice/full harness from Sprint 2. + - Capture baseline wall time and RSS from the latest B.8 artifact. + - Measure Phase 3 wall time separately with tracing or stats. + - Acceptance: Phase 3 over the elspeth module graph adds less than 60s wall + time and less than 500 MiB peak RSS over the existing analyze path. + - If the gate fails, stop with a results memo and propose either weighted-components + default, graph-pruning config, or ADR amendment. +- [x] Run full verification floor. +- [x] Mark completed tasks in this plan with `[x]`. + +**Exit:** E2E, determinism, walking skeleton, MCP membership, docs, and +performance gate are all green. + +```bash +bash tests/e2e/phase3_subsystems.sh +bash tests/e2e/sprint_1_walking_skeleton.sh +cargo fmt --all -- --check +cargo clippy --workspace --all-targets --all-features -- -D warnings +cargo nextest run --workspace --all-features +RUSTDOCFLAGS="-D warnings" cargo doc --workspace --no-deps --all-features +cargo deny check +plugins/python/.venv/bin/ruff check plugins/python +plugins/python/.venv/bin/ruff format --check plugins/python +plugins/python/.venv/bin/mypy --strict plugins/python +plugins/python/.venv/bin/pytest plugins/python/tests -q +``` + +**Commit:** `test(wp4): add subsystem e2e and docs (phase3 task 7)` + +--- + +## Whole-Workstream Exit Criteria + +- ADR-006 default: Leiden clustering over directed weighted `imports` plus + `calls` module graph, seeded from config, deterministic. +- Weighted-components fallback is config-selectable and test-covered. +- Subsystems are persisted as `core:subsystem:{sha256(sorted(member_ids))[0..12]}` + with properties carrying algorithm, seed, resolution, modularity, member IDs, + edge types, and weight policy. +- `in_subsystem` edges link every member module to its subsystem. +- `runs.stats.clustering` records status, config, counts, modularity, duration, + and skip/finding state. +- `CLA-FACT-CLUSTERING-WEAK-MODULARITY` persists when modularity is below 0.3 + and there is an emitted subsystem anchor. +- `subsystem_members(id)` is available through MCP. +- `summary(id)` on a subsystem returns the no-subsystem-summary policy envelope + and does not spend an LLM call. +- New subsystem E2E and determinism tests pass. +- Sprint-1 walking-skeleton E2E still passes. +- ADR-023 floor passes locally. +- Elspeth-slice performance gate is recorded and within the stated envelope, + or implementation stops with a memo and ADR/plan amendment instead of + forcing a red gate through. + +--- + +## Risks and Unknowns + +- **Graph crate suitability.** The current Rust graph ecosystem has several + plausible Leiden crates, but none is a perfect one-line match for + ADR-006 plus weighted-components fallback. Task 1 is intentionally a hard qualification + gate. +- **Directed modularity semantics.** If the selected crate silently treats the + graph as undirected, the adapter test must fail and the plan must be amended. +- **Import resolution precision.** AST import strings do not prove a target + module exists. Host-side filtering against collected module IDs avoids FK + failures but means external imports are skipped for Phase 3. +- **Finding anchoring.** Weak modularity is run-level in meaning but entity- + anchored in the current schema. This plan chooses largest-subsystem anchoring + to avoid a schema break; if reviewers dislike that, decide before Task 5. +- **Analyze orchestrator size.** `analyze.rs` is already large. Tasks 2 and 5 + should extract small helpers instead of growing the main function blindly. +- **Performance.** B.8 measured healthy analyze behavior on the elspeth slice; + Phase 3 must be measured as an incremental cost, not assumed cheap. +- **MCP surface drift.** The plan adds exactly one MCP tool. Any further shape + changes to `neighborhood`, `summary`, or related tools require a plan update + and review before implementation continues. + +--- + +## Phase 1 Self-Review Checklist + +- [x] Current-state audit answers all five handoff questions. +- [x] Design decisions include recommendation, alternatives, and reasons. +- [x] File map lists every planned create/modify target. +- [x] Task breakdown has seven tasks, each sized to a reviewable slice. +- [x] Every task names tests, commands, exit criteria, and commit message. +- [x] Scope exclusions remain respected: no subsystem summarization, no catalog + artifacts, no HTTP API, no multi-language clustering. +- [x] Plan stops before implementation pending human approval. diff --git a/docs/superpowers/plans/2026-05-18-phase3-subsystems.review.json b/docs/superpowers/plans/2026-05-18-phase3-subsystems.review.json new file mode 100644 index 00000000..9f6f08b9 --- /dev/null +++ b/docs/superpowers/plans/2026-05-18-phase3-subsystems.review.json @@ -0,0 +1,45 @@ +{ + "verdict": "APPROVED_WITH_WARNINGS", + "summary": "Focused local plan review after amendment 4668e88. No blockers found for starting Phase 2 after human approval. Two risks remain intentionally gated in Task 1/Task 7.", + "review_mode": "focused-local", + "plan_file": "docs/superpowers/plans/2026-05-18-phase3-subsystems.md", + "reviewed_commit": "4668e88", + "reviewed_at": "2026-05-18T10:25:39Z", + "blocking_issues": [], + "warnings": [ + { + "id": "W1", + "source": "reality", + "issue": "The graph crate recommendation is intentionally provisional. The selected crate must prove directed weighted semantics, fixed-seed determinism, cargo-deny compatibility, and pinned-toolchain compilation in Task 1 before later tasks proceed.", + "resolution": "Task 1 already includes a hard dependency-qualification gate and stop/amend behavior if the crate fails." + }, + { + "id": "W2", + "source": "systems", + "issue": "Phase 3 performance impact on the elspeth module graph is not known until implemented.", + "resolution": "Task 7 includes an explicit performance gate and stop/amend behavior if Phase 3 exceeds the stated wall-time or RSS budget." + } + ], + "recommendations": [ + "Approve the current plan only if Task 1 is treated as a hard gate rather than a routine dependency addition.", + "During implementation, keep imports-edge filtering in Task 3 before writer insertion as amended in commit 4668e88." + ], + "reviewer_summaries": { + "reality": { + "status": "WARNINGS", + "blocking": 0 + }, + "architecture": { + "status": "PASS", + "blocking": 0 + }, + "quality": { + "status": "PASS", + "blocking": 0 + }, + "systems": { + "status": "WARNINGS", + "blocking": 0 + } + } +} diff --git a/plugins/python/plugin.toml b/plugins/python/plugin.toml index 9a5db6d3..add14c44 100644 --- a/plugins/python/plugin.toml +++ b/plugins/python/plugin.toml @@ -1,7 +1,7 @@ [plugin] name = "clarion-plugin-python" plugin_id = "python" -version = "0.1.4" +version = "0.1.5" protocol_version = "1.0" # Bare basename per ADR-021 §Layer 1 + WP2 scrub commit eb0a41d — the host # refuses manifests whose `executable` carries any path component. @@ -31,19 +31,20 @@ pin = "1.1.409" [ontology] # Sprint 2 B.2: classes + modules join the kind set. B.3 (ADR-026) adds # the first edge kind, `contains`. B.4* adds scan-time `calls` edges. -# B.5* adds scan-time `references` edges. +# B.5* adds scan-time `references` edges. Phase 3 Task 3 adds scan-time +# `imports` candidate edges. entity_kinds = ["function", "class", "module"] -edge_kinds = ["contains", "calls", "references"] +edge_kinds = ["contains", "calls", "references", "imports"] # Per ADR-022: uppercase `CLA-{PLUGIN_ID_UPPER}-`. Reserved at parse # against the CLA-INFRA-* and CLA-FACT-* namespaces. rule_id_prefix = "CLA-PY-" -# Bumps per ADR-027 when the entity/edge/rule set shifts. B.5* is a MINOR -# bump (additive `references` edge kind). NOTE: ADR-007's summary-cache key +# Bumps per ADR-027 when the entity/edge/rule set shifts. Phase 3 Task 3 is a +# MINOR bump (additive `imports` edge kind). NOTE: ADR-007's summary-cache key # is the 5-tuple (entity_id, content_hash, prompt_template_id, model_tier, # guidance_fingerprint) — ontology_version is handshake-validation, NOT a # cache-key component. New edge rows miss the cache by component-1 of # the 5-tuple organically (no edges live in the 5-tuple yet anyway). -ontology_version = "0.5.0" +ontology_version = "0.6.0" [integrations.wardline] # Verified present in Wardline source (src/wardline/core/registry.py:55, diff --git a/plugins/python/pyproject.toml b/plugins/python/pyproject.toml index 2418218b..d7ff461b 100644 --- a/plugins/python/pyproject.toml +++ b/plugins/python/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "clarion-plugin-python" -version = "0.1.4" +version = "0.1.5" description = "Clarion Python language plugin — walking-skeleton v0.1 baseline" readme = "README.md" requires-python = ">=3.11" diff --git a/plugins/python/src/clarion_plugin_python/__init__.py b/plugins/python/src/clarion_plugin_python/__init__.py index 1147de55..52a28586 100644 --- a/plugins/python/src/clarion_plugin_python/__init__.py +++ b/plugins/python/src/clarion_plugin_python/__init__.py @@ -1,3 +1,3 @@ """clarion-plugin-python — Python language plugin for Clarion.""" -__version__ = "0.1.4" +__version__ = "0.1.5" diff --git a/plugins/python/src/clarion_plugin_python/call_resolver.py b/plugins/python/src/clarion_plugin_python/call_resolver.py index f79e563e..7b12c98b 100644 --- a/plugins/python/src/clarion_plugin_python/call_resolver.py +++ b/plugins/python/src/clarion_plugin_python/call_resolver.py @@ -43,6 +43,7 @@ class CallResolutionResult: unresolved_call_sites_total: int = 0 unresolved_call_sites: list[UnresolvedCallSite] = field(default_factory=list) pyright_query_latency_ms: list[int] = field(default_factory=list) + pyright_index_parse_latency_ms: list[int] = field(default_factory=list) findings: list[Finding] = field(default_factory=list) diff --git a/plugins/python/src/clarion_plugin_python/extractor.py b/plugins/python/src/clarion_plugin_python/extractor.py index 93306bd3..50d1f86e 100644 --- a/plugins/python/src/clarion_plugin_python/extractor.py +++ b/plugins/python/src/clarion_plugin_python/extractor.py @@ -2,8 +2,8 @@ Walks a parsed Python file and emits one ``module`` entity per file plus one ``function`` entity per ``FunctionDef`` / ``AsyncFunctionDef`` and one -``class`` entity per ``ClassDef``. Decorator, import, and call-edge emission is -later WP3-feature-complete scope. +``class`` entity per ``ClassDef``. It also emits anchored scan-time +``imports``, ``calls``, and ``references`` candidate edges. Entity shape matches the Rust host's ``RawEntity`` + ``RawSource`` contract (``crates/clarion-core/src/plugin/host.rs:132-154``):: @@ -57,6 +57,7 @@ import ast import sys +import time from dataclasses import dataclass, field from pathlib import PurePosixPath from typing import Literal, NotRequired, TypedDict, cast @@ -131,7 +132,13 @@ class RawEdge(TypedDict): source_byte_start: NotRequired[int] source_byte_end: NotRequired[int] confidence: NotRequired[Literal["resolved", "ambiguous", "inferred"]] - properties: NotRequired[CallsEdgeProperties | ReferencesEdgeProperties] + properties: NotRequired[CallsEdgeProperties | ReferencesEdgeProperties | ImportsEdgeProperties] + + +class ImportsEdgeProperties(TypedDict): + imported_name: str + import_style: Literal["import", "from_import"] + level: int @dataclass @@ -144,7 +151,10 @@ class ExtractionStats: references_skipped_cap_total: int = 0 unresolved_reference_sites_total: int = 0 pyright_query_latency_ms: list[int] = field(default_factory=list) + pyright_index_parse_latency_ms: list[int] = field(default_factory=list) + extractor_parse_latency_ms: int = 0 findings: list[Finding] = field(default_factory=list) + duplicate_entities_dropped_total: int = 0 @classmethod def from_resolution_results( @@ -164,6 +174,10 @@ def from_resolution_results( *calls.pyright_query_latency_ms, *references.pyright_query_latency_ms, ], + pyright_index_parse_latency_ms=[ + *calls.pyright_index_parse_latency_ms, + *references.pyright_index_parse_latency_ms, + ], findings=[*calls.findings, *references.findings], ) @@ -280,9 +294,21 @@ def extract_with_stats( callers can supply a project-relative path here while keeping ``file_path`` absolute so the host's path jail validates the original path. + + Same-id collisions (PEP-484 ``@overload`` stubs, ``singledispatch`` + ``def _(...):`` sequences, intentional redefinitions) are resolved at + the emit boundary so the host's ``UNIQUE(entities.id)`` never trips + mid-run. ``@overload`` stubs are recognised and dropped *before* the + walk descends — their bodies (``...``) carry only type-checker hints + so signature references are also suppressed. Any other duplicates + that survive (e.g. aliased ``from typing import overload as o``, + ``singledispatch.register`` users writing ``def _():`` repeatedly) + are deduplicated first-wins with a stderr line per drop and + ``ExtractionStats.duplicate_entities_dropped_total`` bumped per drop. """ prefix_source = module_prefix_path if module_prefix_path is not None else file_path dotted_module = module_dotted_name(prefix_source) + is_package_module = PurePosixPath(prefix_source).name == "__init__.py" # Top-level __init__.py would resolve to "" — entity_id() rejects that # (crates/clarion-core/src/entity_id.rs:97-101). Skip with stderr. @@ -293,9 +319,11 @@ def extract_with_stats( ) return ExtractResult([], [], ExtractionStats()) + parse_started_ns = time.perf_counter_ns() try: tree = ast.parse(source) except SyntaxError as exc: + parse_latency_ms = _elapsed_ms(parse_started_ns) sys.stderr.write( f"clarion-plugin-python: skipping {file_path}: syntax error at " f"line {exc.lineno}: {exc.msg}\n", @@ -303,13 +331,15 @@ def extract_with_stats( return ExtractResult( [_build_module_entity(source, dotted_module, file_path, "syntax_error")], [], - ExtractionStats(), + ExtractionStats(extractor_parse_latency_ms=parse_latency_ms), ) + parse_latency_ms = _elapsed_ms(parse_started_ns) module_entity = _build_module_entity(source, dotted_module, file_path, "ok") entities: list[RawEntity] = [module_entity] edges: list[RawEdge] = [] function_ids: list[str] = [] + walk_state = _WalkState(seen_ids={module_entity["id"]}, file_path=file_path) _walk( tree, [tree], @@ -319,17 +349,173 @@ def extract_with_stats( entities, edges, function_ids, + walk_state, + ) + edges.extend( + _collect_import_edges( + source, + tree, + dotted_module, + module_entity["id"], + is_package_module=is_package_module, + ), ) reference_sites = _collect_reference_sites(source, tree, dotted_module, module_entity["id"]) call_stats = call_resolver.resolve_calls(file_path, function_ids) reference_stats = reference_resolver.resolve_references(file_path, reference_sites) edges.extend(cast("list[RawEdge]", call_stats.edges)) edges.extend(cast("list[RawEdge]", reference_stats.edges)) - return ExtractResult( - entities, - edges, - ExtractionStats.from_resolution_results(call_stats, reference_stats), + stats = ExtractionStats.from_resolution_results(call_stats, reference_stats) + stats.extractor_parse_latency_ms = parse_latency_ms + stats.duplicate_entities_dropped_total = walk_state.duplicate_entities_dropped + return ExtractResult(entities, edges, stats) + + +def _elapsed_ms(started_ns: int) -> int: + return max(1, (time.perf_counter_ns() - started_ns + 999_999) // 1_000_000) + + +def _collect_import_edges( + source: str, + tree: ast.Module, + dotted_module: str, + module_entity_id: str, + *, + is_package_module: bool, +) -> list[RawEdge]: + collector = _ImportEdgeCollector( + source, + dotted_module, + module_entity_id, + is_package_module=is_package_module, + ) + collector.visit(tree) + return collector.edges + + +class _ImportEdgeCollector(ast.NodeVisitor): + def __init__( + self, + source: str, + dotted_module: str, + module_entity_id: str, + *, + is_package_module: bool, + ) -> None: + self.source = source + self.dotted_module = dotted_module + self.module_entity_id = module_entity_id + self.is_package_module = is_package_module + self.edges: list[RawEdge] = [] + + def visit_Import(self, node: ast.Import) -> None: + source_byte_start, source_byte_end = _node_byte_range(self.source, node) + for alias in node.names: + self.edges.append( + self._edge( + target_module=alias.name, + imported_name=alias.name, + import_style="import", + level=0, + source_range=(source_byte_start, source_byte_end), + ), + ) + + def visit_ImportFrom(self, node: ast.ImportFrom) -> None: + source_byte_start, source_byte_end = _node_byte_range(self.source, node) + for alias in node.names: + target_module = _import_from_target( + self.dotted_module, + node.module, + node.level, + alias.name, + is_package_module=self.is_package_module, + ) + if target_module is None: + continue + self.edges.append( + self._edge( + target_module=target_module, + imported_name=alias.name, + import_style="from_import", + level=node.level, + source_range=(source_byte_start, source_byte_end), + ), + ) + + def _edge( + self, + *, + target_module: str, + imported_name: str, + import_style: Literal["import", "from_import"], + level: int, + source_range: tuple[int, int], + ) -> RawEdge: + source_byte_start, source_byte_end = source_range + return { + "kind": "imports", + "from_id": self.module_entity_id, + "to_id": entity_id(_PLUGIN_ID, "module", target_module), + "source_byte_start": source_byte_start, + "source_byte_end": source_byte_end, + "confidence": "resolved", + "properties": { + "imported_name": imported_name, + "import_style": import_style, + "level": level, + }, + } + + +def _import_from_target( + dotted_module: str, + module: str | None, + level: int, + imported_name: str, + *, + is_package_module: bool, +) -> str | None: + if level == 0: + return module + + base_parts = _relative_import_base_parts( + dotted_module, + level, + is_package_module=is_package_module, ) + if base_parts is None: + return None + + target_parts = [*base_parts] + if module: + target_parts.extend(part for part in module.split(".") if part) + elif imported_name != "*": + target_parts.append(imported_name) + + return ".".join(target_parts) if target_parts else None + + +def _relative_import_base_parts( + dotted_module: str, + level: int, + *, + is_package_module: bool, +) -> list[str] | None: + all_parts = dotted_module.split(".") + package_parts = all_parts if is_package_module else all_parts[:-1] + keep = len(package_parts) - (level - 1) + if keep < 0: + return None + return package_parts[:keep] + + +def _node_byte_range(source: str, node: ast.Import | ast.ImportFrom) -> tuple[int, int]: + line_starts = _line_starts(source) + start_line = node.lineno - 1 + end_line = (node.end_lineno or node.lineno) - 1 + end_col = node.end_col_offset if node.end_col_offset is not None else node.col_offset + return line_starts[start_line] + node.col_offset, line_starts[end_line] + end_col def _collect_reference_sites( @@ -368,6 +554,12 @@ def visit_AsyncFunctionDef(self, node: ast.AsyncFunctionDef) -> None: self._visit_function(node) def _visit_function(self, node: ast.FunctionDef | ast.AsyncFunctionDef) -> None: + # PEP 484 stub: signature annotations are type-checker hints, not + # references the consult-mode briefing cares about; the body is `...`. + # Skipping keeps reference-site ownership consistent with `_walk` (no + # entity for the stub → nothing to attribute references to). + if _has_overload_decorator(node): + return function_id = self._entity_id_for_scope("function", node) self.owner_stack.append(function_id) self.bound_stack.append(_scope_local_names(node)) @@ -531,6 +723,43 @@ def visit_Name(self, node: ast.Name) -> None: self.names.add(node.id) +@dataclass +class _WalkState: + """Mutable accumulator threaded through ``_walk`` for cross-cutting bookkeeping. + + ``seen_ids`` is seeded with the module-entity id by ``extract_with_stats`` + so the safety net catches the (degenerate) case of a function colliding + with the module's id. ``duplicate_entities_dropped`` is bumped once per + same-id drop; the caller copies it into ``ExtractionStats``. + """ + + seen_ids: set[str] + file_path: str + duplicate_entities_dropped: int = 0 + + +def _has_overload_decorator(node: ast.FunctionDef | ast.AsyncFunctionDef) -> bool: + """Return True if ``node`` is decorated with ``@overload`` (PEP 484 stub). + + Recognises three import-name forms in source: bare ``@overload`` (from + ``from typing import overload``), ``@typing.overload``, and + ``@typing_extensions.overload``. Aliased re-imports such as + ``from typing import overload as o`` defeat this pattern-based check — + the safety-net dedup in ``_walk`` catches the resulting same-id + collision and keeps the run alive. + """ + for decorator in node.decorator_list: + match decorator: + case ast.Name(id="overload"): + return True + case ast.Attribute( + value=ast.Name(id="typing" | "typing_extensions"), + attr="overload", + ): + return True + return False + + def _walk( # noqa: PLR0913 - recursive walker needs both accumulators + parent context (B.3) node: ast.AST, parents: list[ast.AST], @@ -540,6 +769,7 @@ def _walk( # noqa: PLR0913 - recursive walker needs both accumulators + parent out_entities: list[RawEntity], out_edges: list[RawEdge], out_function_ids: list[str], + state: _WalkState, ) -> None: """Recursively walk ``node``'s AST children, emitting entities + contains edges. @@ -549,14 +779,36 @@ def _walk( # noqa: PLR0913 - recursive walker needs both accumulators + parent own id as the new parent — so grandchildren get the right ``from_id`` on their contains edge (B.3 Q3: emitter is exhaustive, never transitive). + + Two stub-skip rules keep the host's ``UNIQUE(entities.id)`` from + tripping. (1) ``@overload``-decorated functions are recognised + semantically: skip emission, skip recursion (PEP 484 stub bodies are + ``...``). The implementation appears last in source order and emits + normally. (2) Any other surviving same-id collision (aliased + ``overload`` imports, ``singledispatch.register`` ``def _():`` + sequences, manual redefinition) is dropped first-wins with a stderr + line and a ``state.duplicate_entities_dropped`` bump. Recursion into + the dropped child is suppressed too: its nested entities would carry + a parent_id whose entity the host never sees. """ for child in ast.iter_child_nodes(node): new_parent_id = parent_entity_id match child: case ast.FunctionDef() | ast.AsyncFunctionDef(): + if _has_overload_decorator(child): + continue entity, child_id = _build_function_entity( child, parents, dotted_module, file_path, parent_entity_id ) + if child_id in state.seen_ids: + state.duplicate_entities_dropped += 1 + sys.stderr.write( + f"clarion-plugin-python: dropping duplicate entity {child_id} " + f"in {state.file_path} at line {child.lineno} " + f"(first definition wins)\n", + ) + continue + state.seen_ids.add(child_id) out_entities.append(entity) out_edges.append(_contains_edge(parent_entity_id, child_id)) out_function_ids.append(child_id) @@ -565,6 +817,15 @@ def _walk( # noqa: PLR0913 - recursive walker needs both accumulators + parent entity, child_id = _build_class_entity( child, parents, dotted_module, file_path, parent_entity_id ) + if child_id in state.seen_ids: + state.duplicate_entities_dropped += 1 + sys.stderr.write( + f"clarion-plugin-python: dropping duplicate entity {child_id} " + f"in {state.file_path} at line {child.lineno} " + f"(first definition wins)\n", + ) + continue + state.seen_ids.add(child_id) out_entities.append(entity) out_edges.append(_contains_edge(parent_entity_id, child_id)) new_parent_id = child_id @@ -577,6 +838,7 @@ def _walk( # noqa: PLR0913 - recursive walker needs both accumulators + parent out_entities, out_edges, out_function_ids, + state, ) diff --git a/plugins/python/src/clarion_plugin_python/pyright_session.py b/plugins/python/src/clarion_plugin_python/pyright_session.py index 305edb21..b7909d4c 100644 --- a/plugins/python/src/clarion_plugin_python/pyright_session.py +++ b/plugins/python/src/clarion_plugin_python/pyright_session.py @@ -94,6 +94,7 @@ class _EntityInfo: class _FunctionIndex: source: str line_starts: tuple[int, ...] + parse_latency_ms: int module_id: str by_id: dict[str, _FunctionInfo] by_name_position: dict[tuple[int, int], _FunctionInfo] @@ -143,6 +144,7 @@ def __init__( # noqa: PLR0913 - knobs are tested lifecycle boundaries. self._disabled = False self._findings: list[Finding] = [] self._function_indexes: dict[Path, _FunctionIndex] = {} + self._index_parse_latency_ms: list[int] = [] def __enter__(self) -> Self: return self @@ -190,11 +192,15 @@ def resolve_calls( ] ast_call_sites_total = sum(len(function.call_sites) for function in requested) if not requested: - return CallResolutionResult(findings=self._pop_findings()) + return CallResolutionResult( + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), + findings=self._pop_findings(), + ) if not self._ensure_process(): return CallResolutionResult( unresolved_call_sites_total=ast_call_sites_total, + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), findings=self._pop_findings(), ) @@ -222,6 +228,7 @@ def resolve_calls( unresolved_call_sites_total=unresolved, unresolved_call_sites=unresolved_sites, pyright_query_latency_ms=[latency_ms], + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), findings=self._pop_findings(), ) @@ -234,7 +241,10 @@ def resolve_references( index = self._function_index_for_path(path) reference_sites_total = len(sites) if not sites: - return ReferenceResolutionResult(findings=self._pop_findings()) + return ReferenceResolutionResult( + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), + findings=self._pop_findings(), + ) if reference_sites_total > self.max_reference_sites_per_file: self._record_finding( FINDING_PYRIGHT_REFERENCE_SITE_CAP, @@ -246,12 +256,14 @@ def resolve_references( reference_sites_total=reference_sites_total, references_skipped_cap_total=reference_sites_total, unresolved_reference_sites_total=reference_sites_total, + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), findings=self._pop_findings(), ) if not self._ensure_process(): return ReferenceResolutionResult( reference_sites_total=reference_sites_total, unresolved_reference_sites_total=reference_sites_total, + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), findings=self._pop_findings(), ) @@ -287,6 +299,7 @@ def resolve_references( references_skipped_external_total=skipped_external, unresolved_reference_sites_total=unresolved, pyright_query_latency_ms=[latency_ms], + pyright_index_parse_latency_ms=self._pop_index_parse_latencies(), findings=self._pop_findings(), ) @@ -739,6 +752,7 @@ def _function_index_for_path(self, path: Path) -> _FunctionIndex: source = resolved.read_text(encoding="utf-8") index = _build_function_index(self.project_root, resolved, source) self._function_indexes[resolved] = index + self._index_parse_latency_ms.append(index.parse_latency_ms) return index def _record_finding(self, subcode: str, message: str, **metadata: object) -> None: @@ -756,11 +770,18 @@ def _pop_findings(self) -> list[Finding]: self._findings = [] return findings + def _pop_index_parse_latencies(self) -> list[int]: + latencies = self._index_parse_latency_ms + self._index_parse_latency_ms = [] + return latencies + def _build_function_index(project_root: Path, path: Path, source: str) -> _FunctionIndex: relative = path.relative_to(project_root) if path.is_relative_to(project_root) else path dotted_module = module_dotted_name(relative.as_posix()) + parse_started = time.perf_counter() tree = ast.parse(source) + parse_latency_ms = max(1, math.ceil((time.perf_counter() - parse_started) * 1000)) functions: list[_FunctionInfo] = [] entities: list[_EntityInfo] = [] source_lines = source.splitlines() @@ -777,6 +798,7 @@ def _build_function_index(project_root: Path, path: Path, source: str) -> _Funct return _FunctionIndex( source=source, line_starts=line_starts, + parse_latency_ms=parse_latency_ms, module_id=module_id, by_id=by_id, by_name_position=by_name_position, diff --git a/plugins/python/src/clarion_plugin_python/qualname.py b/plugins/python/src/clarion_plugin_python/qualname.py index 3b7ce290..96efd1c1 100644 --- a/plugins/python/src/clarion_plugin_python/qualname.py +++ b/plugins/python/src/clarion_plugin_python/qualname.py @@ -13,9 +13,11 @@ class definition has been executed; Clarion's static analyser has to prepends ``parent..`` — the ```` marker distinguishes a closure from a method. -The L7 lock-in (``wp3-python-plugin.md §L7``) is that Clarion's Python -plugin and Wardline's annotations must produce the same string here; -divergence breaks the cross-product identity join (ADR-018). +The L7 lock-in (``wp3-python-plugin.md §L7``) is that Clarion reconstructs +the same bare Python ``__qualname__`` semantics that Wardline stores in its +``FingerprintEntry.qualified_name`` field. Clarion entity names prepend the +dotted module path elsewhere; ADR-018 requires cross-product joins to translate +between those shapes instead of comparing strings directly. Sprint 1 covers ``FunctionDef`` and ``AsyncFunctionDef`` as emitted entities; ``ClassDef`` is recognised as a parent scope only (class diff --git a/plugins/python/src/clarion_plugin_python/reference_resolver.py b/plugins/python/src/clarion_plugin_python/reference_resolver.py index 0fcc8bd0..a4077996 100644 --- a/plugins/python/src/clarion_plugin_python/reference_resolver.py +++ b/plugins/python/src/clarion_plugin_python/reference_resolver.py @@ -48,6 +48,7 @@ class ReferenceResolutionResult: references_skipped_cap_total: int = 0 unresolved_reference_sites_total: int = 0 pyright_query_latency_ms: list[int] = field(default_factory=list) + pyright_index_parse_latency_ms: list[int] = field(default_factory=list) findings: list[Finding] = field(default_factory=list) diff --git a/plugins/python/src/clarion_plugin_python/server.py b/plugins/python/src/clarion_plugin_python/server.py index cc00cdc1..912d9470 100644 --- a/plugins/python/src/clarion_plugin_python/server.py +++ b/plugins/python/src/clarion_plugin_python/server.py @@ -33,7 +33,7 @@ from clarion_plugin_python.stdout_guard import install_stdio from clarion_plugin_python.wardline_probe import probe as wardline_probe -ONTOLOGY_VERSION = "0.5.0" +ONTOLOGY_VERSION = "0.6.0" # Sprint 1 defaults for the Wardline version pin (WP3 L8 + plugin.toml # `[integrations.wardline]`). Kept as module constants so Task 7's @@ -185,6 +185,8 @@ def handle_analyze_file(params: dict[str, Any], state: ServerState) -> dict[str, "references_skipped_cap_total": 0, "unresolved_reference_sites_total": 0, "pyright_query_latency_ms": [], + "pyright_index_parse_latency_ms": [], + "extractor_parse_latency_ms": 0, } file_path_raw = params.get("file_path") if not isinstance(file_path_raw, str): @@ -217,6 +219,8 @@ def handle_analyze_file(params: dict[str, Any], state: ServerState) -> dict[str, "references_skipped_cap_total": result.stats.references_skipped_cap_total, "unresolved_reference_sites_total": result.stats.unresolved_reference_sites_total, "pyright_query_latency_ms": result.stats.pyright_query_latency_ms, + "pyright_index_parse_latency_ms": result.stats.pyright_index_parse_latency_ms, + "extractor_parse_latency_ms": result.stats.extractor_parse_latency_ms, } return {"entities": result.entities, "edges": result.edges, "stats": stats} diff --git a/plugins/python/tests/test_extractor.py b/plugins/python/tests/test_extractor.py index 49f520ba..76a9bfa4 100644 --- a/plugins/python/tests/test_extractor.py +++ b/plugins/python/tests/test_extractor.py @@ -113,6 +113,10 @@ def _call_edges(edges: Sequence[RawEdge]) -> list[RawEdge]: return [edge for edge in edges if edge["kind"] == "calls"] +def _import_edges(edges: Sequence[RawEdge]) -> list[RawEdge]: + return [edge for edge in edges if edge["kind"] == "imports"] + + def _reference_sites_for(source: str) -> list[ReferenceSite]: resolver = RecordingReferenceResolver() extract_with_stats(source, "demo.py", reference_resolver=resolver) @@ -252,6 +256,179 @@ def test_extractor_with_noop_resolver_emits_no_calls() -> None: assert [edge for edge in edges if edge["kind"] == "calls"] == [] +def test_import_statement_emits_module_import_edge() -> None: + _entities, edges = extract("import pkg.service\n", "consumer.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:consumer", + "to_id": "python:module:pkg.service", + "source_byte_start": 0, + "source_byte_end": len(b"import pkg.service"), + "confidence": "resolved", + "properties": { + "imported_name": "pkg.service", + "import_style": "import", + "level": 0, + }, + }, + ] + + +def test_from_import_emits_import_edge_to_parent_module() -> None: + _entities, edges = extract("from pkg.service import Client\n", "consumer.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:consumer", + "to_id": "python:module:pkg.service", + "source_byte_start": 0, + "source_byte_end": len(b"from pkg.service import Client"), + "confidence": "resolved", + "properties": { + "imported_name": "Client", + "import_style": "from_import", + "level": 0, + }, + }, + ] + + +def test_multi_name_from_import_emits_one_edge_per_imported_name() -> None: + source = "from pkg.service import Client, helper, CONSTANT\n" + _entities, edges = extract(source, "consumer.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:consumer", + "to_id": "python:module:pkg.service", + "source_byte_start": 0, + "source_byte_end": len(b"from pkg.service import Client, helper, CONSTANT"), + "confidence": "resolved", + "properties": { + "imported_name": imported_name, + "import_style": "from_import", + "level": 0, + }, + } + for imported_name in ("Client", "helper", "CONSTANT") + ] + + +def test_relative_import_emits_package_relative_module_edge() -> None: + _entities, edges = extract("from . import sibling\n", "pkg/consumer.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:pkg.consumer", + "to_id": "python:module:pkg.sibling", + "source_byte_start": 0, + "source_byte_end": len(b"from . import sibling"), + "confidence": "resolved", + "properties": { + "imported_name": "sibling", + "import_style": "from_import", + "level": 1, + }, + }, + ] + + +def test_relative_import_from_package_init_targets_sibling_module() -> None: + _entities, edges = extract("from . import sibling\n", "pkg/__init__.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:pkg", + "to_id": "python:module:pkg.sibling", + "source_byte_start": 0, + "source_byte_end": len(b"from . import sibling"), + "confidence": "resolved", + "properties": { + "imported_name": "sibling", + "import_style": "from_import", + "level": 1, + }, + }, + ] + + +def test_level_two_relative_import_from_package_init_targets_parent_sibling() -> None: + _entities, edges = extract("from .. import sibling\n", "pkg/sub/__init__.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:pkg.sub", + "to_id": "python:module:pkg.sibling", + "source_byte_start": 0, + "source_byte_end": len(b"from .. import sibling"), + "confidence": "resolved", + "properties": { + "imported_name": "sibling", + "import_style": "from_import", + "level": 2, + }, + }, + ] + + +def test_level_two_relative_import_module_from_package_init_targets_parent_module() -> None: + _entities, edges = extract("from ..other import x\n", "pkg/sub/__init__.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:pkg.sub", + "to_id": "python:module:pkg.other", + "source_byte_start": 0, + "source_byte_end": len(b"from ..other import x"), + "confidence": "resolved", + "properties": { + "imported_name": "x", + "import_style": "from_import", + "level": 2, + }, + }, + ] + + +def test_level_three_relative_import_from_deep_package_init_targets_root_sibling() -> None: + _entities, edges = extract("from ... import x\n", "pkg/sub/deeper/__init__.py") + + assert _import_edges(edges) == [ + { + "kind": "imports", + "from_id": "python:module:pkg.sub.deeper", + "to_id": "python:module:pkg.x", + "source_byte_start": 0, + "source_byte_end": len(b"from ... import x"), + "confidence": "resolved", + "properties": { + "imported_name": "x", + "import_style": "from_import", + "level": 3, + }, + }, + ] + + +def test_import_edges_have_source_byte_range_and_resolved_confidence() -> None: + source = "é = 1\nimport pkg.service\n" + _entities, edges = extract(source, "consumer.py") + import_edge = _import_edges(edges)[0] + + expected_start = len("é = 1\n".encode()) + assert import_edge["source_byte_start"] == expected_start + assert import_edge["source_byte_end"] == expected_start + len(b"import pkg.service") + assert import_edge["confidence"] == "resolved" + + def test_extractor_appends_calls_from_resolver_and_carries_stats() -> None: result = extract_with_stats( "def callee():\n pass\n\ndef caller():\n callee()\n", @@ -280,6 +457,8 @@ def test_extractor_appends_calls_from_resolver_and_carries_stats() -> None: }, ] assert result.stats.pyright_query_latency_ms == [17] + assert result.stats.pyright_index_parse_latency_ms == [] + assert result.stats.extractor_parse_latency_ms > 0 @pytest.mark.pyright @@ -833,3 +1012,187 @@ def test_every_non_module_entity_has_matching_contains_edge() -> None: continue pair = (entity["parent_id"], entity["id"]) assert pair in edge_pairs, f"missing contains edge for {entity['id']}" + + +# ── @typing.overload disposition (clarion-e29402d1ba) ────────────────────────── + + +def test_module_overload_collapses_to_implementation_entity() -> None: + """`@overload` stubs share a qualname with the implementation; only the impl is callable. + + Per PEP 484 the stub signatures are type-checker hints — emitting them as + entities collides on the host's UNIQUE(entities.id). Plugin must skip the + stubs and emit one function entity whose source range is the implementation. + """ + source = ( + "from typing import overload\n" + "\n" + "@overload\n" + "def foo(x: int) -> int: ...\n" + "@overload\n" + "def foo(x: str) -> str: ...\n" + "def foo(x):\n" + " return x\n" + ) + entities, edges = extract(source, "demo.py") + function_entities = [e for e in entities if e["kind"] == "function"] + assert len(function_entities) == 1 + fn = function_entities[0] + assert fn["id"] == "python:function:demo.foo" + # Source range points at the implementation (the `def foo(x):` at line 7), not a stub. + assert fn["source"]["source_range"]["start_line"] == 7 + # Exactly one contains edge for the function. + contains_edges = [e for e in edges if e["kind"] == "contains"] + assert contains_edges == [ + {"kind": "contains", "from_id": "python:module:demo", "to_id": fn["id"]}, + ] + + +def test_method_overload_collapses_to_implementation_entity_elspeth_reproducer() -> None: + """Exact shape of elspeth ExecutionRepository.complete_node_state (3 stubs + impl).""" + source = ( + "from typing import overload\n" + "\n" + "class ExecutionRepository:\n" + " @overload\n" + " def complete_node_state(self, status: int) -> int: ...\n" + " @overload\n" + " def complete_node_state(self, status: str) -> str: ...\n" + " @overload\n" + " def complete_node_state(self, status: bool) -> bool: ...\n" + " def complete_node_state(self, status):\n" + " return status\n" + ) + entities, _ = extract(source, "demo.py") + function_ids = [e["id"] for e in entities if e["kind"] == "function"] + assert function_ids == [ + "python:function:demo.ExecutionRepository.complete_node_state", + ] + + +def test_qualified_typing_overload_is_recognised() -> None: + """`@typing.overload` attribute form must also collapse stubs.""" + source = ( + "import typing\n" + "\n" + "@typing.overload\n" + "def foo(x: int) -> int: ...\n" + "@typing.overload\n" + "def foo(x: str) -> str: ...\n" + "def foo(x):\n" + " return x\n" + ) + entities, _ = extract(source, "demo.py") + function_ids = [e["id"] for e in entities if e["kind"] == "function"] + assert function_ids == ["python:function:demo.foo"] + + +def test_typing_extensions_overload_is_recognised() -> None: + """`@typing_extensions.overload` is the same protocol as typing.overload.""" + source = ( + "import typing_extensions\n" + "\n" + "@typing_extensions.overload\n" + "def foo(x: int) -> int: ...\n" + "def foo(x):\n" + " return x\n" + ) + entities, _ = extract(source, "demo.py") + function_ids = [e["id"] for e in entities if e["kind"] == "function"] + assert function_ids == ["python:function:demo.foo"] + + +def test_async_overload_is_recognised() -> None: + """`async def` overloads collapse the same way as sync `def`.""" + source = ( + "from typing import overload\n" + "\n" + "@overload\n" + "async def foo(x: int) -> int: ...\n" + "async def foo(x):\n" + " return x\n" + ) + entities, _ = extract(source, "demo.py") + function_ids = [e["id"] for e in entities if e["kind"] == "function"] + assert function_ids == ["python:function:demo.foo"] + + +def test_overload_stub_with_extra_decorators_is_still_skipped() -> None: + """A function carrying `@overload` alongside other decorators is still a stub.""" + source = ( + "from typing import overload\n" + "\n" + "class Foo:\n" + " @staticmethod\n" + " @overload\n" + " def bar(x: int) -> int: ...\n" + " @staticmethod\n" + " def bar(x):\n" + " return x\n" + ) + entities, _ = extract(source, "demo.py") + function_ids = [e["id"] for e in entities if e["kind"] == "function"] + assert function_ids == ["python:function:demo.Foo.bar"] + + +def test_references_inside_overload_implementation_body_are_emitted() -> None: + """Skipping stub bodies must not suppress reference collection inside the impl.""" + source = ( + "from typing import overload\n" + "\n" + "@overload\n" + "def foo(x: int) -> int: ...\n" + "def foo(x):\n" + " return BAR\n" + ) + sites = _reference_sites_for(source) + # `overload` import is referenced by the decorators on stubs; those should still surface + # at the module level. The key assertion is that the impl's body reference to `BAR` + # is attributed to the implementation function, not lost. + impl_sites = [s for s in sites if s.from_id == "python:function:demo.foo"] + assert len(impl_sites) == 1 + assert impl_sites[0].kind == "name" + + +def test_safety_net_drops_duplicate_non_overload_definitions( + capsys: pytest.CaptureFixture[str], +) -> None: + """Two non-overload defs sharing a qualname (rare but legal Python) must not crash the run. + + Example pattern in the wild: `@singledispatch.register` users frequently write + `def _(arg): ...` repeatedly at the same scope. First-wins, stderr-logged, + counter bumped, and the host never sees a duplicate id. + """ + source = ( + "def helper(x):\n" + " return x + 1\n" + "\n" + "def helper(x):\n" # redefinition shadows the first; same qualname. + " return x * 2\n" + ) + result = extract_with_stats(source, "demo.py") + function_entities = [e for e in result.entities if e["kind"] == "function"] + assert len(function_entities) == 1, "duplicate ids deduped at the emit boundary" + assert function_entities[0]["id"] == "python:function:demo.helper" + # First-wins: source range points at the first def (line 1), not the second. + assert function_entities[0]["source"]["source_range"]["start_line"] == 1 + assert result.stats.duplicate_entities_dropped_total == 1 + err = capsys.readouterr().err + assert "python:function:demo.helper" in err + assert "demo.py" in err + + +def test_safety_net_drops_contains_edges_to_dropped_entities() -> None: + """A contains edge pointing at a dropped duplicate must also be dropped.""" + source = "def helper(x):\n return x\n\ndef helper(x):\n return x\n" + result = extract_with_stats(source, "demo.py") + # Both defs are top-level so contains-edges would be (module → helper) twice; + # after dedup, exactly one survives. + contains_edges = [e for e in result.edges if e["kind"] == "contains"] + assert contains_edges == [ + { + "kind": "contains", + "from_id": "python:module:demo", + "to_id": "python:function:demo.helper", + }, + ] diff --git a/plugins/python/tests/test_package.py b/plugins/python/tests/test_package.py index 0abab77c..a1fe5820 100644 --- a/plugins/python/tests/test_package.py +++ b/plugins/python/tests/test_package.py @@ -11,12 +11,12 @@ def test_package_version_matches_pyproject() -> None: - assert clarion_plugin_python.__version__ == "0.1.4" + assert clarion_plugin_python.__version__ == "0.1.5" def test_manifest_declares_references_edge_kind() -> None: manifest = tomllib.loads((_PLUGIN_ROOT / "plugin.toml").read_text(encoding="utf-8")) - assert manifest["plugin"]["version"] == "0.1.4" - assert manifest["ontology"]["ontology_version"] == "0.5.0" - assert manifest["ontology"]["edge_kinds"] == ["contains", "calls", "references"] + assert manifest["plugin"]["version"] == "0.1.5" + assert manifest["ontology"]["ontology_version"] == "0.6.0" + assert manifest["ontology"]["edge_kinds"] == ["contains", "calls", "references", "imports"] diff --git a/plugins/python/tests/test_pyright_session.py b/plugins/python/tests/test_pyright_session.py index 9934f29e..4a4cf8df 100644 --- a/plugins/python/tests/test_pyright_session.py +++ b/plugins/python/tests/test_pyright_session.py @@ -117,6 +117,7 @@ def caller(): ] assert result.edges[0]["source_byte_start"] < result.edges[0]["source_byte_end"] assert result.pyright_query_latency_ms[0] > 0 + assert result.pyright_index_parse_latency_ms[0] > 0 assert result.unresolved_call_sites_total == 0 diff --git a/plugins/python/tests/test_round_trip.py b/plugins/python/tests/test_round_trip.py index 45b7997f..869108cc 100644 --- a/plugins/python/tests/test_round_trip.py +++ b/plugins/python/tests/test_round_trip.py @@ -163,9 +163,11 @@ def test_round_trip_self_analysis() -> None: # noqa: PLR0915 - by-kind invarian contains_pairs = {(e["from_id"], e["to_id"]) for e in edges if e["kind"] == "contains"} calls_edges = [e for e in edges if e["kind"] == "calls"] references_edges = [e for e in edges if e["kind"] == "references"] + imports_edges = [e for e in edges if e["kind"] == "imports"] resolved_calls = [e for e in calls_edges if e["confidence"] == "resolved"] ambiguous_calls = [e for e in calls_edges if e["confidence"] == "ambiguous"] resolved_references = [e for e in references_edges if e["confidence"] == "resolved"] + assert imports_edges, "extractor.py self-analysis must emit import candidate edges" assert resolved_calls, "extractor.py self-analysis must emit at least one resolved call" assert resolved_references, ( "extractor.py self-analysis must emit at least one resolved references edge" @@ -178,7 +180,7 @@ def test_round_trip_self_analysis() -> None: # noqa: PLR0915 - by-kind invarian # Contains edges MUST NOT carry source range fields (ADR-026 §3). assert "source_byte_start" not in edge assert "source_byte_end" not in edge - elif edge["kind"] in {"calls", "references"}: + elif edge["kind"] in {"calls", "references", "imports"}: assert edge["source_byte_start"] < edge["source_byte_end"] assert edge["confidence"] in {"resolved", "ambiguous"} else: diff --git a/plugins/python/tests/test_server.py b/plugins/python/tests/test_server.py index ea0a1769..b89a91d7 100644 --- a/plugins/python/tests/test_server.py +++ b/plugins/python/tests/test_server.py @@ -81,8 +81,8 @@ def test_initialize_roundtrip() -> None: assert response["id"] == 1 result = response["result"] assert result["name"] == "clarion-plugin-python" - assert result["version"] == "0.1.4" - assert result["ontology_version"] == "0.5.0" + assert result["version"] == "0.1.5" + assert result["ontology_version"] == "0.6.0" # Capabilities carry the L8 Wardline probe result. We don't pin a # specific status here because the probe's output depends on whether # wardline is installed in the test environment — all three legal @@ -326,6 +326,7 @@ def resolve_calls( }, ], pyright_query_latency_ms=[11, 29], + pyright_index_parse_latency_ms=[5], ) def resolve_references( @@ -353,6 +354,7 @@ def resolve_references( references_skipped_cap_total=3, unresolved_reference_sites_total=4, pyright_query_latency_ms=[31], + pyright_index_parse_latency_ms=[7], ) def close(self) -> None: @@ -365,7 +367,11 @@ def close(self) -> None: response = server_module.handle_analyze_file({"file_path": str(demo)}, state) - assert response["stats"] == { + stats = response["stats"] + extractor_parse_latency_ms = stats.pop("extractor_parse_latency_ms") + assert isinstance(extractor_parse_latency_ms, int) + assert extractor_parse_latency_ms > 0 + assert stats == { "unresolved_call_sites_total": 3, "unresolved_call_sites": [ { @@ -382,6 +388,7 @@ def close(self) -> None: "references_skipped_cap_total": 3, "unresolved_reference_sites_total": 4, "pyright_query_latency_ms": [11, 29, 31], + "pyright_index_parse_latency_ms": [5, 7], } assert any(edge["kind"] == "references" for edge in response["edges"]) diff --git a/scripts/check-migration-retirement.py b/scripts/check-migration-retirement.py new file mode 100644 index 00000000..8278735f --- /dev/null +++ b/scripts/check-migration-retirement.py @@ -0,0 +1,141 @@ +#!/usr/bin/env python3 +"""Guard ADR-024's in-place migration retirement trigger. + +Before the first external published build, Clarion may edit migration 0001 in +place. After that trigger fires, add: + + crates/clarion-storage/migrations/published_build.txt + +with the git ref of the first published build whose 0001 migration must stay +stable. Once the marker exists, this guard fails if the working tree's 0001 +differs from that ref; later schema changes must be additive 0002+ migrations. +""" + +from __future__ import annotations + +import argparse +import subprocess +import sys +import tempfile +from pathlib import Path + +MIGRATION_PATH = Path("crates/clarion-storage/migrations/0001_initial_schema.sql") +MARKER_PATH = Path("crates/clarion-storage/migrations/published_build.txt") + + +class CheckError(Exception): + """Raised for guard failures.""" + + +def git(root: Path, *args: str) -> subprocess.CompletedProcess[str]: + return subprocess.run( + ["git", *args], + cwd=root, + check=False, + text=True, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + + +def git_ok(root: Path, *args: str) -> None: + proc = git(root, *args) + if proc.returncode != 0: + raise CheckError( + f"git {' '.join(args)} failed:\nstdout:\n{proc.stdout}\nstderr:\n{proc.stderr}" + ) + + +def first_marker_ref(root: Path, marker_path: Path = MARKER_PATH) -> str | None: + marker = root / marker_path + if not marker.exists(): + return None + for raw_line in marker.read_text(encoding="utf-8").splitlines(): + line = raw_line.strip() + if line and not line.startswith("#"): + return line + raise CheckError(f"{marker_path} exists but does not name a git ref") + + +def migration_text_at_ref(root: Path, ref: str, migration_path: Path = MIGRATION_PATH) -> str: + proc = git(root, "show", f"{ref}:{migration_path.as_posix()}") + if proc.returncode != 0: + raise CheckError( + f"{MARKER_PATH} names {ref!r}, but git cannot read " + f"{migration_path} at that ref:\n{proc.stderr}" + ) + return proc.stdout + + +def check(root: Path) -> None: + ref = first_marker_ref(root) + if ref is None: + print(f"{MARKER_PATH} absent; ADR-024 in-place migration policy is still pre-trigger.") + return + + migration = root / MIGRATION_PATH + if not migration.exists(): + raise CheckError(f"{MIGRATION_PATH} is missing") + + current = migration.read_text(encoding="utf-8") + published = migration_text_at_ref(root, ref) + if current != published: + raise CheckError( + f"{MIGRATION_PATH} differs from published marker {ref!r}. " + "ADR-024 has retired in-place edits; add a 0002+ migration instead." + ) + print(f"{MIGRATION_PATH} matches published marker {ref!r}.") + + +def write(path: Path, text: str) -> None: + path.parent.mkdir(parents=True, exist_ok=True) + path.write_text(text, encoding="utf-8") + + +def run_self_test() -> None: + with tempfile.TemporaryDirectory() as tmp: + root = Path(tmp) + git_ok(root, "init", "-q") + git_ok(root, "config", "user.email", "clarion-test@example.invalid") + git_ok(root, "config", "user.name", "Clarion Test") + + write(root / MIGRATION_PATH, "initial migration\n") + git_ok(root, "add", MIGRATION_PATH.as_posix()) + git_ok(root, "commit", "-q", "-m", "initial migration") + git_ok(root, "tag", "published-build") + + check(root) + + write(root / MARKER_PATH, "published-build\n") + check(root) + + write(root / MIGRATION_PATH, "edited migration\n") + try: + check(root) + except CheckError as exc: + if "0002+" not in str(exc): + raise + else: + raise CheckError("self-test expected edited 0001 to fail after marker") + + print("migration retirement guard self-test passed") + + +def main(argv: list[str]) -> int: + parser = argparse.ArgumentParser() + parser.add_argument("--self-test", action="store_true", help="run built-in guard tests") + args = parser.parse_args(argv) + + try: + if args.self_test: + run_self_test() + else: + check(Path.cwd()) + except CheckError as exc: + print(f"migration retirement guard failed: {exc}", file=sys.stderr) + return 1 + return 0 + + +if __name__ == "__main__": + raise SystemExit(main(sys.argv[1:])) diff --git a/scripts/check-python-ontology-version.py b/scripts/check-python-ontology-version.py new file mode 100644 index 00000000..fc8fdf1f --- /dev/null +++ b/scripts/check-python-ontology-version.py @@ -0,0 +1,122 @@ +#!/usr/bin/env python3 +"""Guard Python plugin ontology_version lockstep. + +The Python plugin declares the ontology version in two places: + +* plugins/python/plugin.toml, consumed by the Rust host during discovery. +* clarion_plugin_python.server.ONTOLOGY_VERSION, returned during initialize. + +Those values are intentionally duplicated so the plugin can answer the JSON-RPC +handshake without parsing its installed manifest at runtime. This CI guard keeps +the duplication mechanical. +""" + +from __future__ import annotations + +import argparse +import ast +import sys +import tempfile +import tomllib +from pathlib import Path + +DEFAULT_MANIFEST = Path("plugins/python/plugin.toml") +DEFAULT_SERVER = Path("plugins/python/src/clarion_plugin_python/server.py") + + +class CheckError(Exception): + """Raised when the ontology-version guard fails.""" + + +def manifest_ontology_version(manifest_path: Path) -> str: + manifest = tomllib.loads(manifest_path.read_text(encoding="utf-8")) + try: + version = manifest["ontology"]["ontology_version"] + except KeyError as exc: + raise CheckError(f"{manifest_path} is missing [ontology].ontology_version") from exc + if not isinstance(version, str) or not version.strip(): + raise CheckError(f"{manifest_path} has invalid ontology_version {version!r}") + return version + + +def server_ontology_version(server_path: Path) -> str: + module = ast.parse(server_path.read_text(encoding="utf-8"), filename=str(server_path)) + for node in module.body: + if isinstance(node, ast.Assign) and any( + isinstance(target, ast.Name) and target.id == "ONTOLOGY_VERSION" + for target in node.targets + ): + if isinstance(node.value, ast.Constant) and isinstance(node.value.value, str): + return node.value.value + raise CheckError(f"{server_path}: ONTOLOGY_VERSION must be a string literal") + if ( + isinstance(node, ast.AnnAssign) + and isinstance(node.target, ast.Name) + and node.target.id == "ONTOLOGY_VERSION" + ): + if isinstance(node.value, ast.Constant) and isinstance(node.value.value, str): + return node.value.value + raise CheckError(f"{server_path}: ONTOLOGY_VERSION must be a string literal") + raise CheckError(f"{server_path} does not define ONTOLOGY_VERSION") + + +def check(manifest_path: Path, server_path: Path) -> str: + manifest_version = manifest_ontology_version(manifest_path) + server_version = server_ontology_version(server_path) + if manifest_version != server_version: + raise CheckError( + "Python plugin ontology_version drift: " + f"{manifest_path} has {manifest_version!r}, " + f"{server_path} has {server_version!r}" + ) + return manifest_version + + +def write(path: Path, text: str) -> None: + path.parent.mkdir(parents=True, exist_ok=True) + path.write_text(text, encoding="utf-8") + + +def run_self_test() -> None: + with tempfile.TemporaryDirectory() as tmp: + root = Path(tmp) + manifest = root / "plugin.toml" + server = root / "server.py" + + write(manifest, '[ontology]\nontology_version = "1.2.3"\n') + write(server, 'ONTOLOGY_VERSION = "1.2.3"\n') + assert check(manifest, server) == "1.2.3" + + write(server, 'ONTOLOGY_VERSION = "1.2.4"\n') + try: + check(manifest, server) + except CheckError as exc: + if "ontology_version drift" not in str(exc): + raise + else: + raise CheckError("self-test expected ontology_version mismatch to fail") + + print("Python ontology_version guard self-test passed") + + +def main(argv: list[str]) -> int: + parser = argparse.ArgumentParser(description="Check Python plugin ontology_version lockstep") + parser.add_argument("--manifest", type=Path, default=DEFAULT_MANIFEST) + parser.add_argument("--server", type=Path, default=DEFAULT_SERVER) + parser.add_argument("--self-test", action="store_true", help="run built-in guard tests") + args = parser.parse_args(argv) + + try: + if args.self_test: + run_self_test() + else: + version = check(args.manifest, args.server) + print(f"Python plugin ontology_version matches: {version}") + except CheckError as exc: + print(f"Python ontology_version guard failed: {exc}", file=sys.stderr) + return 1 + return 0 + + +if __name__ == "__main__": + raise SystemExit(main(sys.argv[1:])) diff --git a/tests/e2e/phase3_subsystems.sh b/tests/e2e/phase3_subsystems.sh new file mode 100755 index 00000000..72bb1c36 --- /dev/null +++ b/tests/e2e/phase3_subsystems.sh @@ -0,0 +1,252 @@ +#!/usr/bin/env bash +# Phase 3 subsystem clustering end-to-end test. +# +# Builds a real Clarion database through `clarion analyze`, verifies persisted +# subsystem entities / membership edges / clustering stats, checks deterministic +# subsystem signatures across two clean project copies, and exercises the MCP +# `subsystem_members` tool over stdio. + +set -euo pipefail + +REPO_ROOT="${REPO_ROOT:-$(git rev-parse --show-toplevel)}" +VENV="${VENV:-$REPO_ROOT/plugins/python/.venv}" +CARGO_BUILD="${CARGO_BUILD:-1}" +MIN_CLUSTER_SIZE=2 + +log() { printf '[phase3-subsystems] %s\n' "$*" >&2; } +fail() { printf '[phase3-subsystems] FAIL: %s\n' "$*" >&2; exit 1; } + +cd "$REPO_ROOT" + +if [ "$CARGO_BUILD" = "1" ]; then + log "building clarion (release) ..." + cargo build --workspace --release +fi +CLARION_BIN="$REPO_ROOT/target/release/clarion" +[ -x "$CLARION_BIN" ] || fail "clarion binary missing at $CLARION_BIN" + +if [ ! -d "$VENV" ]; then + log "creating venv at $VENV ..." + python3 -m venv "$VENV" +fi +log "installing clarion-plugin-python (editable) ..." +"$VENV/bin/pip" install --quiet -e "$REPO_ROOT/plugins/python[dev]" +PLUGIN_BIN="$VENV/bin/clarion-plugin-python" +[ -x "$PLUGIN_BIN" ] || fail "clarion-plugin-python missing at $PLUGIN_BIN" + +ROOT="$(mktemp -d -t clarion-phase3-XXXXXX)" +trap 'rm -rf "$ROOT"' EXIT +PROJECT_A="$ROOT/project-a" +PROJECT_B="$ROOT/project-b" + +write_fixture() { + local dest="$1" + mkdir -p "$dest/pkg/auth" "$dest/pkg/billing" + : > "$dest/pkg/__init__.py" + : > "$dest/pkg/auth/__init__.py" + : > "$dest/pkg/billing/__init__.py" + cat > "$dest/pkg/auth/login.py" <<'PY' +from pkg.auth import policy, token + +def login(user: str) -> str: + return token.issue(policy.normalize(user)) +PY + cat > "$dest/pkg/auth/token.py" <<'PY' +from pkg.auth import policy + +def issue(user: str) -> str: + return f"token:{policy.normalize(user)}" +PY + cat > "$dest/pkg/auth/policy.py" <<'PY' +from pkg.auth import token + +def normalize(user: str) -> str: + return user.strip().lower() + +def preview(user: str) -> str: + return token.issue(user) +PY + cat > "$dest/pkg/billing/invoice.py" <<'PY' +from pkg.billing import ledger, tax + +def create(amount: int) -> int: + return ledger.record(tax.apply(amount)) +PY + cat > "$dest/pkg/billing/ledger.py" <<'PY' +from pkg.billing import tax + +def record(amount: int) -> int: + return tax.apply(amount) +PY + cat > "$dest/pkg/billing/tax.py" <<'PY' +from pkg.billing import ledger + +def apply(amount: int) -> int: + return amount + 1 + +def preview(amount: int) -> int: + return ledger.record(amount) +PY + cat > "$dest/clarion.yaml" <&2 || true + fail "expected at least two subsystem rows; got $SUBSYSTEM_COUNT" +fi + +UNDER_MIN=$(sqlite3 "$DB_A" \ + "SELECT COUNT(*) FROM ( \ + SELECT to_id, COUNT(*) AS members \ + FROM edges \ + WHERE kind = 'in_subsystem' \ + GROUP BY to_id \ + HAVING members < $MIN_CLUSTER_SIZE \ + );") +if [ "$UNDER_MIN" != "0" ]; then + sqlite3 "$DB_A" \ + "SELECT to_id, COUNT(*) FROM edges WHERE kind = 'in_subsystem' GROUP BY to_id;" >&2 || true + fail "every subsystem should have at least min_cluster_size=$MIN_CLUSTER_SIZE members" +fi + +CLUSTERING_STATUS=$(sqlite3 "$DB_A" \ + "SELECT json_extract(stats, '\$.clustering.status') FROM runs ORDER BY started_at DESC LIMIT 1;") +if [ "$CLUSTERING_STATUS" != "completed" ]; then + sqlite3 "$DB_A" "SELECT id, status, stats FROM runs;" >&2 || true + fail "expected runs.stats.clustering.status=completed; got $CLUSTERING_STATUS" +fi +CLUSTERING_ALGORITHM=$(sqlite3 "$DB_A" \ + "SELECT json_extract(stats, '\$.clustering.algorithm') FROM runs ORDER BY started_at DESC LIMIT 1;") +if [ "$CLUSTERING_ALGORITHM" != "weighted_components" ]; then + sqlite3 "$DB_A" "SELECT id, status, stats FROM runs;" >&2 || true + fail "expected runs.stats.clustering.algorithm=weighted_components; got $CLUSTERING_ALGORITHM" +fi + +log "verifying deterministic subsystem signature across clean runs ..." +SIG_A="$(subsystem_signature "$DB_A")" +SIG_B="$(subsystem_signature "$DB_B")" +if [ "$SIG_A" != "$SIG_B" ]; then + fail "$(printf 'subsystem signatures differ:\nA:\n%s\nB:\n%s' "$SIG_A" "$SIG_B")" +fi + +log "driving MCP subsystem_members ..." +python3 - "$CLARION_BIN" "$PROJECT_A" <<'PY' +import json +import sqlite3 +import subprocess +import sys +from pathlib import Path + +clarion_bin = Path(sys.argv[1]) +project_dir = Path(sys.argv[2]) +conn = sqlite3.connect(project_dir / ".clarion" / "clarion.db") +subsystem_id = conn.execute( + "SELECT id FROM entities WHERE kind = 'subsystem' ORDER BY id LIMIT 1" +).fetchone()[0] +conn.close() + + +def write_frame(proc: subprocess.Popen[bytes], message: dict[str, object]) -> None: + body = json.dumps(message, separators=(",", ":")).encode("utf-8") + assert proc.stdin is not None + proc.stdin.write(b"Content-Length: " + str(len(body)).encode("ascii") + b"\r\n\r\n") + proc.stdin.write(body) + proc.stdin.flush() + + +def read_frame(proc: subprocess.Popen[bytes]) -> dict[str, object]: + assert proc.stdout is not None + headers: dict[str, str] = {} + while True: + line = proc.stdout.readline() + if line == b"": + stderr = proc.stderr.read().decode("utf-8", "replace") if proc.stderr else "" + raise AssertionError(f"server closed stdout; stderr={stderr}") + if line == b"\r\n": + break + name, value = line.decode("ascii").strip().split(":", 1) + headers[name.lower()] = value.strip() + return json.loads(proc.stdout.read(int(headers["content-length"]))) + + +proc = subprocess.Popen( + [str(clarion_bin), "serve", "--path", str(project_dir)], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, +) +try: + write_frame( + proc, + { + "jsonrpc": "2.0", + "id": "init", + "method": "initialize", + "params": { + "protocolVersion": "2025-11-25", + "capabilities": {}, + "clientInfo": {"name": "phase3-e2e", "version": "0.0.0"}, + }, + }, + ) + read_frame(proc) + write_frame( + proc, + { + "jsonrpc": "2.0", + "id": "members", + "method": "tools/call", + "params": { + "name": "subsystem_members", + "arguments": {"id": subsystem_id}, + }, + }, + ) + response = read_frame(proc) + text = response["result"]["content"][0]["text"] + envelope = json.loads(text) + assert envelope["ok"] is True, envelope + assert envelope["result"]["subsystem"]["id"] == subsystem_id, envelope + assert len(envelope["result"]["members"]) >= 2, envelope +finally: + assert proc.stdin is not None + proc.stdin.close() + proc.wait(timeout=5) +PY + +log "phase3 subsystem e2e passed" diff --git a/tests/e2e/sprint_2_mcp_surface.sh b/tests/e2e/sprint_2_mcp_surface.sh index 4d543761..5d76072f 100755 --- a/tests/e2e/sprint_2_mcp_surface.sh +++ b/tests/e2e/sprint_2_mcp_surface.sh @@ -3,7 +3,7 @@ # # Builds a real demo Clarion database through `clarion analyze`, starts # `clarion serve`, and sends Content-Length framed MCP JSON-RPC requests for -# the seven MCP navigation tools. Filigree is represented by a local HTTP +# the eight MCP navigation tools. Filigree is represented by a local HTTP # server that implements the B.7 reverse entity-association route. set -euo pipefail @@ -378,7 +378,7 @@ finally: assert responses["initialize"]["result"]["protocolVersion"] == "2025-11-25" tools = responses["tools"]["result"]["tools"] -assert len(tools) == 7, tools +assert len(tools) == 8, tools assert [tool["name"] for tool in tools] == [ "entity_at", "find_entity", @@ -387,6 +387,7 @@ assert [tool["name"] for tool in tools] == [ "summary", "issues_for", "neighborhood", + "subsystem_members", ] assert "leaf scope only" in tools[4]["description"] @@ -440,4 +441,4 @@ assert "python:function:demo.world" in filigree_requests, filigree_requests assert "python:function:demo.hello" in filigree_requests, filigree_requests PY -log "PASS: MCP stdio surface returned seven tool responses" +log "PASS: MCP stdio surface returned eight tool definitions and seven tool responses" diff --git a/tests/perf/b8_scale_test/derive-elspeth-corpus.sh b/tests/perf/b8_scale_test/derive-elspeth-corpus.sh new file mode 100755 index 00000000..2e7a7848 --- /dev/null +++ b/tests/perf/b8_scale_test/derive-elspeth-corpus.sh @@ -0,0 +1,50 @@ +#!/usr/bin/env bash +set -euo pipefail + +usage() { + cat >&2 <<'USAGE' +Usage: derive-elspeth-corpus.sh + +Copies the Python source corpus used by the B.8/Phase 3 scale gate into a clean +directory while recording the elspeth commit and dirty status that produced it. +Git worktrees are accepted. The corpus includes tracked and untracked .py files +visible to git; inspect elspeth-dirty-status.txt when reproducing a dirty source +checkout. The output directory must not already exist. +USAGE +} + +if [[ $# -ne 2 ]]; then + usage + exit 2 +fi + +elspeth_root=$1 +output_dir=$2 + +if ! git -C "$elspeth_root" rev-parse --is-inside-work-tree >/dev/null 2>&1; then + echo "elspeth checkout not found: $elspeth_root" >&2 + exit 1 +fi + +if [[ -e "$output_dir" ]]; then + echo "output directory already exists: $output_dir" >&2 + exit 1 +fi + +mkdir -p "$output_dir" +elspeth_root=$(cd "$elspeth_root" && pwd -P) +output_dir=$(cd "$output_dir" && pwd -P) + +git -C "$elspeth_root" rev-parse HEAD >"$output_dir/elspeth-commit.txt" +git -C "$elspeth_root" status --short >"$output_dir/elspeth-dirty-status.txt" + +git -C "$elspeth_root" ls-files -co --exclude-standard '*.py' \ + | sort \ + | while IFS= read -r relative_path; do + source_path="$elspeth_root/$relative_path" + mkdir -p "$output_dir/$(dirname "$relative_path")" + cp -p "$source_path" "$output_dir/$relative_path" + done + +find "$output_dir" -type f -name '*.py' | sort >"$output_dir/corpus-copy.txt" +echo "$output_dir" diff --git a/tests/perf/b8_scale_test/driver.py b/tests/perf/b8_scale_test/driver.py new file mode 100644 index 00000000..24d0e11c --- /dev/null +++ b/tests/perf/b8_scale_test/driver.py @@ -0,0 +1,816 @@ +#!/usr/bin/env python3 +"""B.8 scale-test MCP driver. + +The driver assumes `clarion analyze` has already produced `.clarion/clarion.db` +for the project under test. It starts `clarion serve`, sends Content-Length +framed MCP requests, and writes JSON measurements for the B.8 result memo. +""" + +from __future__ import annotations + +import argparse +import dataclasses +import json +import math +import os +import select +import sqlite3 +import subprocess +import time +from collections import defaultdict +from dataclasses import dataclass +from pathlib import Path +from typing import Any + + +@dataclass(frozen=True) +class CallRecord: + pattern: str + tool: str + phase: str + cache_state: str + latency_ms: float + response_bytes: int + estimated_response_tokens: int + ok: bool + error: bool + unavailable: bool + useful_result: bool + cache_hit: bool | None + unavailable_reason: str | None + stats_delta: dict[str, Any] + truncated: bool = False + label: str | None = None + + +@dataclass(frozen=True) +class ToolRequest: + pattern: str + label: str + tool: str + phase: str + cache_state: str + arguments: dict[str, Any] + + +@dataclass(frozen=True) +class QueryTargets: + entity_at: list[dict[str, Any]] + find_patterns: list[str] + caller_targets: list[str] + path_roots: list[str] + summary_ids: list[str] + issues_ids: list[str] + neighborhood_ids: list[str] + inferred_targets: list[str] + + +def percentile(values: list[float], percent: int) -> float | None: + """Return an upper-biased nearest-rank percentile. + + The upper bias is intentional for tail-latency reporting: a four-sample p50 + should not understate the slower half of the observed calls. + """ + + if not values: + return None + ordered = sorted(values) + index = math.ceil((percent / 100.0) * (len(ordered) + 1)) - 1 + index = max(0, min(index, len(ordered) - 1)) + return round(ordered[index], 3) + + +def _kb(byte_count: int) -> float: + return round(byte_count / 1024.0, 3) + + +def _cache_hit_from_result(result: Any) -> bool | None: + if not isinstance(result, dict) or "cache" not in result: + return None + cache = result["cache"] + if isinstance(cache, dict) and isinstance(cache.get("hit"), bool): + return bool(cache["hit"]) + if isinstance(cache, str): + if cache == "hit": + return True + if cache in {"miss", "cold", "disabled"}: + return False + return None + + +def _estimated_tokens(response_bytes: int) -> int: + return max(1, math.ceil(response_bytes / 4)) + + +def _has_useful_result(tool: str, result: Any) -> bool: + if not isinstance(result, dict) or result.get("available") is False: + return False + keys_by_tool = { + "entity_at": ("entity",), + "find_entity": ("entities",), + "callers_of": ("callers",), + "execution_paths_from": ("paths",), + "summary": ("summary",), + "issues_for": ("matched", "drifted", "not_found"), + "neighborhood": ("callers", "callees", "container", "contained", "references"), + } + for key in keys_by_tool.get(tool, ()): + value = result.get(key) + if value not in (None, [], {}, ""): + return True + return False + + +def parse_tool_response( + pattern: str, + tool: str, + phase: str, + cache_state: str, + response: dict[str, Any], + latency_ms: float, + response_bytes: int, + label: str | None = None, +) -> CallRecord: + if response.get("error") is not None: + return CallRecord( + pattern, + tool, + phase, + cache_state, + round(latency_ms, 3), + response_bytes, + _estimated_tokens(response_bytes), + False, + True, + False, + False, + None, + None, + {}, + False, + label, + ) + + envelope: dict[str, Any] = {} + try: + content = response["result"]["content"] + text = content[0]["text"] + envelope = json.loads(text) + except (KeyError, IndexError, TypeError, json.JSONDecodeError): + return CallRecord( + pattern, + tool, + phase, + cache_state, + round(latency_ms, 3), + response_bytes, + _estimated_tokens(response_bytes), + False, + True, + False, + False, + None, + None, + {}, + False, + label, + ) + + result = envelope.get("result") + result_obj = result if isinstance(result, dict) else {} + unavailable = result_obj.get("available") is False + reason = ( + result_obj.get("reason") if isinstance(result_obj.get("reason"), str) else None + ) + return CallRecord( + pattern=pattern, + tool=tool, + phase=phase, + cache_state=cache_state, + latency_ms=round(latency_ms, 3), + response_bytes=response_bytes, + estimated_response_tokens=_estimated_tokens(response_bytes), + ok=envelope.get("ok") is True, + error=(envelope.get("ok") is not True) or envelope.get("error") is not None, + unavailable=unavailable, + useful_result=_has_useful_result(tool, result_obj), + cache_hit=_cache_hit_from_result(result_obj), + unavailable_reason=reason, + stats_delta=envelope.get("stats_delta") + if isinstance(envelope.get("stats_delta"), dict) + else {}, + truncated=envelope.get("truncated") is True, + label=label, + ) + + +def _summarize_group(records: list[CallRecord]) -> dict[str, Any]: + cache_records = [ + record.cache_hit for record in records if record.cache_hit is not None + ] + tokens_total = 0 + cost_usd = 0.0 + for record in records: + for key in ("summary_tokens_total", "inferred_tokens_total"): + value = record.stats_delta.get(key) + if isinstance(value, int | float): + tokens_total += int(value) + for key in ("summary_cost_usd", "inferred_cost_usd"): + value = record.stats_delta.get(key) + if isinstance(value, int | float): + cost_usd += float(value) + + return { + "call_count": len(records), + "p50_latency_ms": percentile([record.latency_ms for record in records], 50), + "p95_latency_ms": percentile([record.latency_ms for record in records], 95), + "max_latency_ms": max((record.latency_ms for record in records), default=None), + "response_size_p50_kb": _kb( + int(percentile([record.response_bytes for record in records], 50) or 0) + ), + "response_size_p95_kb": _kb( + int(percentile([record.response_bytes for record in records], 95) or 0) + ), + "response_tokens_p50": percentile( + [record.estimated_response_tokens for record in records], 50 + ), + "response_tokens_p95": percentile( + [record.estimated_response_tokens for record in records], 95 + ), + "ok_count": sum(1 for record in records if record.ok), + "available_count": sum( + 1 for record in records if record.ok and not record.unavailable + ), + "useful_result_count": sum(1 for record in records if record.useful_result), + "error_count": sum(1 for record in records if record.error), + "unavailable_count": sum(1 for record in records if record.unavailable), + "truncation_count": sum(1 for record in records if record.truncated), + "summary_cache_hit_rate": ( + round(sum(1 for hit in cache_records if hit) / len(cache_records), 4) + if cache_records + else None + ), + "tokens_total": tokens_total, + "cost_usd": round(cost_usd, 6), + } + + +def summarize_records(records: list[CallRecord]) -> dict[str, Any]: + by_pattern: dict[str, list[CallRecord]] = defaultdict(list) + by_pattern_tool: dict[tuple[str, str], list[CallRecord]] = defaultdict(list) + by_tool: dict[str, list[CallRecord]] = defaultdict(list) + by_phase: dict[str, list[CallRecord]] = defaultdict(list) + for record in records: + by_pattern[record.pattern].append(record) + by_pattern_tool[(record.pattern, record.tool)].append(record) + by_tool[record.tool].append(record) + by_phase[record.phase].append(record) + + pattern_summary: dict[str, Any] = {} + for pattern, pattern_records in sorted(by_pattern.items()): + entry = _summarize_group(pattern_records) + entry["tools"] = { + tool: _summarize_group(tool_records) + for (tool_pattern, tool), tool_records in sorted(by_pattern_tool.items()) + if tool_pattern == pattern + } + pattern_summary[pattern] = entry + + storage_backed_tools = { + "entity_at", + "find_entity", + "callers_of", + "execution_paths_from", + "neighborhood", + } + steady_state_storage = [ + record + for record in records + if record.phase == "steady_state" and record.tool in storage_backed_tools + ] + + return { + "overall": _summarize_group(records), + "by_tool": { + tool: _summarize_group(tool_records) + for tool, tool_records in sorted(by_tool.items()) + }, + "by_phase": { + phase: _summarize_group(phase_records) + for phase, phase_records in sorted(by_phase.items()) + }, + "by_pattern": pattern_summary, + "gate": { + "steady_state_storage_backed": _summarize_group(steady_state_storage), + }, + } + + +def summary_miss_then_hit(records: list[CallRecord]) -> bool: + cold_misses = [ + record + for record in records + if record.tool == "summary" + and record.cache_state == "cold" + and record.cache_hit is False + ] + warm_hits = [ + record + for record in records + if record.tool == "summary" + and record.cache_state == "warm" + and record.cache_hit is True + ] + return bool(cold_misses) and len(warm_hits) >= len(cold_misses) + + +def _read_exact(fd: int, byte_count: int, timeout_seconds: float) -> bytes: + chunks: list[bytes] = [] + remaining = byte_count + deadline = time.monotonic() + timeout_seconds + while remaining: + timeout = deadline - time.monotonic() + if timeout <= 0: + raise TimeoutError(f"timed out reading {byte_count} response bytes") + readable, _, _ = select.select([fd], [], [], timeout) + if not readable: + raise TimeoutError(f"timed out reading {byte_count} response bytes") + chunk = os.read(fd, remaining) + if not chunk: + raise EOFError("server closed stdout") + chunks.append(chunk) + remaining -= len(chunk) + return b"".join(chunks) + + +def read_frame( + proc: subprocess.Popen[bytes], timeout_seconds: float +) -> tuple[dict[str, Any], int]: + if proc.stdout is None: + raise RuntimeError("process stdout not piped") + fd = proc.stdout.fileno() + header = bytearray() + while not header.endswith(b"\r\n\r\n"): + header.extend(_read_exact(fd, 1, timeout_seconds)) + headers: dict[str, str] = {} + for line in bytes(header).decode("ascii").split("\r\n"): + if not line: + continue + name, value = line.split(":", 1) + headers[name.lower()] = value.strip() + length = int(headers["content-length"]) + body = _read_exact(fd, length, timeout_seconds) + return json.loads(body), len(body) + + +def write_frame(proc: subprocess.Popen[bytes], message: dict[str, Any]) -> None: + if proc.stdin is None: + raise RuntimeError("process stdin not piped") + body = json.dumps(message, separators=(",", ":")).encode("utf-8") + proc.stdin.write(b"Content-Length: " + str(len(body)).encode("ascii") + b"\r\n\r\n") + proc.stdin.write(body) + proc.stdin.flush() + + +class McpClient: + def __init__( + self, + clarion_bin: Path, + project: Path, + config: Path | None, + timeout_seconds: float, + ) -> None: + command = [str(clarion_bin), "serve", "--path", str(project)] + if config is not None: + command.extend(["--config", str(config)]) + self.proc = subprocess.Popen( + command, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + self.timeout_seconds = timeout_seconds + + def request(self, message: dict[str, Any]) -> tuple[dict[str, Any], int, float]: + started = time.perf_counter() + write_frame(self.proc, message) + response, size = read_frame(self.proc, self.timeout_seconds) + latency_ms = (time.perf_counter() - started) * 1000.0 + return response, size, latency_ms + + def close(self) -> str: + if self.proc.stdin is not None: + self.proc.stdin.close() + try: + self.proc.wait(timeout=10) + except subprocess.TimeoutExpired: + self.proc.terminate() + self.proc.wait(timeout=10) + stderr = "" + if self.proc.stderr is not None: + stderr = self.proc.stderr.read().decode("utf-8", "replace") + if self.proc.returncode != 0: + raise RuntimeError( + f"clarion serve exited {self.proc.returncode}; stderr={stderr}" + ) + return stderr + + +def _rows( + conn: sqlite3.Connection, query: str, params: tuple[Any, ...] = () +) -> list[sqlite3.Row]: + return list(conn.execute(query, params)) + + +def discover_targets(project: Path) -> QueryTargets: + db_path = project / ".clarion" / "clarion.db" + conn = sqlite3.connect(db_path) + conn.row_factory = sqlite3.Row + try: + entity_rows = _rows( + conn, + """ + SELECT id, kind, short_name, source_file_path, source_line_start + FROM entities + WHERE source_file_path IS NOT NULL AND source_line_start IS NOT NULL + ORDER BY CASE kind WHEN 'function' THEN 0 WHEN 'class' THEN 1 ELSE 2 END, id + LIMIT 200 + """, + ) + entity_at = [] + for row in entity_rows: + source_path = Path(row["source_file_path"]) + try: + file_arg = str(source_path.relative_to(project)) + except ValueError: + file_arg = os.path.relpath(source_path, project) + entity_at.append( + { + "id": row["id"], + "file": file_arg, + "line": int(row["source_line_start"]), + } + ) + + ids = [str(row["id"]) for row in entity_rows] + fallback_id = ids[0] if ids else "" + find_patterns = [ + str(row["short_name"] or row["id"]).split(":")[-1] + for row in entity_rows[:20] + ] + if not find_patterns and fallback_id: + find_patterns = [fallback_id] + + caller_targets = [ + row["to_id"] + for row in _rows( + conn, + "SELECT DISTINCT to_id FROM edges WHERE kind = 'calls' ORDER BY to_id LIMIT 50", + ) + ] + path_roots = [ + row["from_id"] + for row in _rows( + conn, + "SELECT DISTINCT from_id FROM edges WHERE kind = 'calls' ORDER BY from_id LIMIT 50", + ) + ] + summary_ids = [ + row["id"] + for row in _rows( + conn, + "SELECT id FROM entities WHERE content_hash IS NOT NULL ORDER BY id LIMIT 50", + ) + ] + issues_ids = [ + row["id"] + for row in _rows(conn, "SELECT id FROM entities ORDER BY id LIMIT 50") + ] + neighborhood_ids = ids[:50] or issues_ids[:50] + inferred_targets = [ + row["id"] + for row in _rows( + conn, + """ + SELECT DISTINCT e.id + FROM entities e + JOIN entity_unresolved_call_sites s + ON s.callee_expr = e.short_name + OR s.callee_expr LIKE '%' || e.short_name || '%' + ORDER BY e.id + LIMIT 10 + """, + ) + ] + finally: + conn.close() + + def fallback(values: list[str]) -> list[str]: + return values or ([fallback_id] if fallback_id else []) + + return QueryTargets( + entity_at=entity_at, + find_patterns=find_patterns or ["python"], + caller_targets=fallback(caller_targets), + path_roots=fallback(path_roots), + summary_ids=fallback(summary_ids), + issues_ids=fallback(issues_ids), + neighborhood_ids=fallback(neighborhood_ids), + inferred_targets=fallback(inferred_targets), + ) + + +def _cycle(values: list[Any], index: int) -> Any: + if not values: + raise ValueError("no target values available") + return values[index % len(values)] + + +def _request( + pattern: str, + label: str, + tool: str, + phase: str, + cache_state: str, + arguments: dict[str, Any], +) -> ToolRequest: + return ToolRequest( + pattern=pattern, + label=label, + tool=tool, + phase=phase, + cache_state=cache_state, + arguments=arguments, + ) + + +def light_pattern(targets: QueryTargets) -> list[ToolRequest]: + first_entity_at = _cycle(targets.entity_at, 0) + return [ + _request( + "light", + "L01-entity-at", + "entity_at", + "cold_start", + "none", + {"file": first_entity_at["file"], "line": first_entity_at["line"]}, + ), + _request( + "light", + "L02-find-entity", + "find_entity", + "cold_start", + "none", + {"pattern": _cycle(targets.find_patterns, 0), "limit": 10}, + ), + _request( + "light", + "L03-callers-of", + "callers_of", + "cold_start", + "none", + {"id": _cycle(targets.caller_targets, 0)}, + ), + _request( + "light", + "L04-neighborhood", + "neighborhood", + "cold_start", + "none", + {"id": _cycle(targets.neighborhood_ids, 0)}, + ), + _request( + "light", + "L05-entity-at-repeat", + "entity_at", + "cold_start", + "none", + {"file": first_entity_at["file"], "line": first_entity_at["line"]}, + ), + ] + + +def _medium_like( + pattern: str, + targets: QueryTargets, + count: int, + *, + phase: str | None = None, + summary_cache_state: str | None = None, + label_prefix: str | None = None, +) -> list[ToolRequest]: + warm = pattern == "medium-warm" + phase = phase or ("steady_state" if warm else "warmup") + cache_state = summary_cache_state or ("warm" if warm else "cold") + label_prefix = label_prefix or ("MW" if warm else "MC") + manifest = [ + ( + "entity_at", + { + "file": _cycle(targets.entity_at, 0)["file"], + "line": _cycle(targets.entity_at, 0)["line"], + }, + ), + ("find_entity", {"pattern": _cycle(targets.find_patterns, 0), "limit": 20}), + ("callers_of", {"id": _cycle(targets.caller_targets, 0)}), + ("execution_paths_from", {"id": _cycle(targets.path_roots, 0), "max_depth": 3}), + ("summary", {"id": _cycle(targets.summary_ids, 0)}), + ( + "issues_for", + {"id": _cycle(targets.issues_ids, 0), "include_contained": True}, + ), + ("neighborhood", {"id": _cycle(targets.neighborhood_ids, 0)}), + ( + "entity_at", + { + "file": _cycle(targets.entity_at, 1)["file"], + "line": _cycle(targets.entity_at, 1)["line"], + }, + ), + ("find_entity", {"pattern": _cycle(targets.find_patterns, 1), "limit": 20}), + ("callers_of", {"id": _cycle(targets.caller_targets, 1)}), + ("summary", {"id": _cycle(targets.summary_ids, 1)}), + ("neighborhood", {"id": _cycle(targets.neighborhood_ids, 1)}), + ("execution_paths_from", {"id": _cycle(targets.path_roots, 1), "max_depth": 3}), + ( + "issues_for", + {"id": _cycle(targets.issues_ids, 1), "include_contained": False}, + ), + ( + "entity_at", + { + "file": _cycle(targets.entity_at, 2)["file"], + "line": _cycle(targets.entity_at, 2)["line"], + }, + ), + ("find_entity", {"pattern": _cycle(targets.find_patterns, 2), "limit": 20}), + ("summary", {"id": _cycle(targets.summary_ids, 2)}), + ( + "callers_of", + {"id": _cycle(targets.caller_targets, 2), "confidence": "ambiguous"}, + ), + ( + "neighborhood", + {"id": _cycle(targets.neighborhood_ids, 2), "confidence": "ambiguous"}, + ), + ("execution_paths_from", {"id": _cycle(targets.path_roots, 2), "max_depth": 2}), + ] + requests: list[ToolRequest] = [] + for i in range(count): + tool, arguments = manifest[i % len(manifest)] + request_cache_state = cache_state if tool == "summary" else "none" + requests.append( + _request( + pattern, + f"{label_prefix}{i + 1:02d}-{tool.replace('_', '-')}", + tool, + phase, + request_cache_state, + arguments, + ) + ) + return requests + + +def inferred_pattern(targets: QueryTargets) -> list[ToolRequest]: + return [ + _request( + "inferred", + f"callers-inferred-{i}", + "callers_of", + "steady_state", + "inferred", + {"id": target, "confidence": "inferred"}, + ) + for i, target in enumerate(targets.inferred_targets[:5]) + ] + + +def build_requests( + targets: QueryTargets, heavy_count: int, include_inferred: bool +) -> tuple[list[ToolRequest], list[str]]: + requests = [] + skipped = [] + requests.extend(light_pattern(targets)) + requests.extend(_medium_like("medium-cold", targets, 20)) + requests.extend(_medium_like("medium-warm", targets, 20)) + requests.extend( + _medium_like( + "heavy", + targets, + max(50, heavy_count), + phase="steady_state", + summary_cache_state="warm", + label_prefix="H", + ) + ) + if include_inferred and targets.inferred_targets: + requests.extend(inferred_pattern(targets)) + else: + skipped.append("inferred") + return requests, skipped + + +def run_driver(args: argparse.Namespace) -> dict[str, Any]: + project = args.project.resolve() + clarion_bin = args.clarion_bin.resolve() + config = args.config.resolve() if args.config else None + targets = discover_targets(project) + requests, skipped_patterns = build_requests( + targets, args.heavy_count, not args.skip_inferred + ) + + client = McpClient(clarion_bin, project, config, args.timeout_seconds) + records: list[CallRecord] = [] + try: + init_response, _, initialize_latency_ms = client.request( + { + "jsonrpc": "2.0", + "id": "init", + "method": "initialize", + "params": { + "protocolVersion": "2025-11-25", + "capabilities": {}, + "clientInfo": {"name": "clarion-b8-driver", "version": "0.1.0"}, + }, + } + ) + tools_response, _, tools_list_latency_ms = client.request( + {"jsonrpc": "2.0", "id": "tools", "method": "tools/list", "params": {}} + ) + tools = [tool["name"] for tool in tools_response["result"]["tools"]] + + for ordinal, request in enumerate(requests): + message = { + "jsonrpc": "2.0", + "id": f"{request.pattern}-{ordinal}", + "method": "tools/call", + "params": {"name": request.tool, "arguments": request.arguments}, + } + response, response_size, latency_ms = client.request(message) + records.append( + parse_tool_response( + request.pattern, + request.tool, + request.phase, + request.cache_state, + response, + latency_ms, + response_size, + request.label, + ) + ) + finally: + client.close() + + return { + "generated_at_unix": int(time.time()), + "project": str(project), + "clarion_bin": str(clarion_bin), + "config": str(config) if config else None, + "initialize": init_response, + "initialize_latency_ms": round(initialize_latency_ms, 3), + "tools_list_latency_ms": round(tools_list_latency_ms, 3), + "tools": tools, + "skipped_patterns": skipped_patterns, + "manifest": [dataclasses.asdict(request) for request in requests], + "records": [dataclasses.asdict(record) for record in records], + "summary_miss_then_hit": summary_miss_then_hit(records), + "summary": summarize_records(records), + } + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument( + "--project", + type=Path, + required=True, + help="Analyzed project root containing .clarion/clarion.db", + ) + parser.add_argument( + "--clarion-bin", type=Path, default=Path("target/release/clarion") + ) + parser.add_argument( + "--config", type=Path, help="Optional clarion serve config path" + ) + parser.add_argument("--output", type=Path, required=True, help="JSON output path") + parser.add_argument("--heavy-count", type=int, default=50) + parser.add_argument("--timeout-seconds", type=float, default=120.0) + parser.add_argument("--skip-inferred", action="store_true") + return parser + + +def main(argv: list[str] | None = None) -> int: + parser = build_parser() + args = parser.parse_args(argv) + result = run_driver(args) + args.output.parent.mkdir(parents=True, exist_ok=True) + args.output.write_text( + json.dumps(result, indent=2, sort_keys=True), encoding="utf-8" + ) + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze-metrics.json b/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze-metrics.json new file mode 100644 index 00000000..6a6417ae --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze-metrics.json @@ -0,0 +1,94 @@ +{ + "command": [ + "/home/john/clarion/target/release/clarion", + "analyze", + "/tmp/clarion-b8-elspeth-tests-20260517T2156Z" + ], + "peak_rss_bytes": 2033442816, + "peak_rss_mb": 1939.242, + "returncode": 0, + "sample_count": 1698, + "samples_tail": [ + { + "rss_bytes": 153673728, + "t": 442.151 + }, + { + "rss_bytes": 153673728, + "t": 442.414 + }, + { + "rss_bytes": 153673728, + "t": 442.676 + }, + { + "rss_bytes": 153673728, + "t": 442.938 + }, + { + "rss_bytes": 153673728, + "t": 443.203 + }, + { + "rss_bytes": 153673728, + "t": 443.466 + }, + { + "rss_bytes": 153673728, + "t": 443.728 + }, + { + "rss_bytes": 153673728, + "t": 443.991 + }, + { + "rss_bytes": 153673728, + "t": 444.253 + }, + { + "rss_bytes": 141119488, + "t": 444.516 + }, + { + "rss_bytes": 141119488, + "t": 444.781 + }, + { + "rss_bytes": 141119488, + "t": 445.044 + }, + { + "rss_bytes": 141119488, + "t": 445.307 + }, + { + "rss_bytes": 139612160, + "t": 445.571 + }, + { + "rss_bytes": 139612160, + "t": 445.834 + }, + { + "rss_bytes": 139612160, + "t": 446.097 + }, + { + "rss_bytes": 139612160, + "t": 446.363 + }, + { + "rss_bytes": 139612160, + "t": 446.625 + }, + { + "rss_bytes": 139612160, + "t": 446.891 + }, + { + "rss_bytes": 0, + "t": 447.154 + } + ], + "wall_seconds": 447.154 +} \ No newline at end of file diff --git a/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze.stderr b/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze.stderr new file mode 100644 index 00000000..e69de29b diff --git a/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze.stdout b/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze.stdout new file mode 100644 index 00000000..ddd6e4e0 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-17T2156Z/analyze.stdout @@ -0,0 +1,15 @@ +2026-05-17T21:58:02.761145Z WARN skipping plugin: discovery error error=no plugin.toml found for /home/john/clarion/target/release/clarion-plugin-fixture (searched neighbor dir and install-prefix share/) +2026-05-17T21:58:02.761174Z INFO discovered plugin plugin_id=python executable=/home/john/clarion/plugins/python/.venv/bin/clarion-plugin-python +2026-05-17T21:58:02.762551Z INFO source tree walk complete file_count=1037 +2026-05-17T21:58:02.762641Z INFO processing plugin plugin_id=python file_count=1037 +2026-05-17T22:05:24.108180Z WARN plugin host collected findings plugin_id=python finding_count=8 +2026-05-17T22:05:24.108206Z WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:integration.cli.test_instantiate_plugins_value_source._build_yaml_with_model", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "0", "source_byte_end": "3309", "source_byte_start": "2425"} +2026-05-17T22:05:24.108214Z WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:integration.audit.test_pass_through_violation_persists.TestAuditRoundTrip.test_json_extract_returns_per_token_identifiers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "15", "source_byte_end": "6229", "source_byte_start": "5123"} +2026-05-17T22:05:24.108220Z WARN plugin host finding plugin_id=python 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subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "1", "source_byte_end": "276976", "source_byte_start": "275103"} +2026-05-17T22:05:24.108239Z WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "2", "source_byte_end": "276221", "source_byte_start": "275103"} +2026-05-17T22:05:24.108244Z WARN plugin host finding plugin_id=python 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176.938, + "returncode": 1, + "sample_count": 1872, + "samples_tail": [ + { + "rss_bytes": 179212288, + "t": 463.416 + }, + { + "rss_bytes": 181411840, + "t": 463.667 + }, + { + "rss_bytes": 182509568, + "t": 463.917 + }, + { + "rss_bytes": 182947840, + "t": 464.167 + }, + { + "rss_bytes": 182947840, + "t": 464.417 + }, + { + "rss_bytes": 185532416, + "t": 464.667 + }, + { + "rss_bytes": 185532416, + "t": 464.917 + }, + { + "rss_bytes": 185532416, + "t": 465.168 + }, + { + "rss_bytes": 185532416, + "t": 465.418 + }, + { + "rss_bytes": 185532416, + "t": 465.668 + }, + { + "rss_bytes": 185532416, + "t": 465.918 + }, + { + "rss_bytes": 185532416, + "t": 466.168 + }, + { + "rss_bytes": 185532416, + "t": 466.418 + }, + { + "rss_bytes": 185532416, + "t": 466.669 + }, + { + "rss_bytes": 185532416, + "t": 466.919 + }, + { + "rss_bytes": 185532416, + "t": 467.169 + }, + { + "rss_bytes": 185532416, + "t": 467.419 + }, + { + "rss_bytes": 185532416, + "t": 467.669 + }, + { + "rss_bytes": 185532416, + "t": 467.92 + }, + { + "rss_bytes": 0, + "t": 468.17 + } + ], + "wall_seconds": 468.17 +} \ No newline at end of file diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze-with-rss.py b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze-with-rss.py new file mode 100644 index 00000000..e44df106 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze-with-rss.py @@ -0,0 +1,95 @@ +#!/usr/bin/env python3 +"""Run clarion analyze and sample peak RSS for B.8 measurement. + +Mirrors the analyze-metrics.json schema from the 2026-05-17 B.8 run. +""" + +from __future__ import annotations + +import json +import os +import subprocess +import sys +import time +from pathlib import Path + + +def _rss_bytes_for_tree(root_pid: int) -> int: + """Sum VmRSS across the process and its descendants.""" + pids = [root_pid] + try: + with open(f"/proc/{root_pid}/task/{root_pid}/children", "r") as fh: + for child_pid in fh.read().split(): + pids.append(int(child_pid)) + except FileNotFoundError: + pass + # one more level for plugin grandchildren (pyright etc.) + expanded = list(pids) + for pid in pids[1:]: + try: + with open(f"/proc/{pid}/task/{pid}/children", "r") as fh: + for child_pid in fh.read().split(): + expanded.append(int(child_pid)) + except FileNotFoundError: + pass + total = 0 + for pid in expanded: + try: + with open(f"/proc/{pid}/status", "r") as fh: + for line in fh: + if line.startswith("VmRSS:"): + kib = int(line.split()[1]) + total += kib * 1024 + break + except FileNotFoundError: + continue + return total + + +def main() -> int: + if len(sys.argv) < 3: + print("usage: analyze-with-rss.py [args...]") + return 2 + output = Path(sys.argv[1]) + cmd = sys.argv[2:] + + env = os.environ.copy() + plugin_bin_dir = "/home/john/clarion/plugins/python/.venv/bin" + env["PATH"] = plugin_bin_dir + ":" + env.get("PATH", "") + + start = time.monotonic() + proc = subprocess.Popen(cmd, env=env) + samples: list[dict[str, float | int]] = [] + peak = 0 + try: + while True: + ret = proc.poll() + now = time.monotonic() - start + rss = _rss_bytes_for_tree(proc.pid) + samples.append({"t": round(now, 3), "rss_bytes": rss}) + if rss > peak: + peak = rss + if ret is not None: + break + time.sleep(0.25) + except KeyboardInterrupt: + proc.terminate() + raise + wall = time.monotonic() - start + rc = proc.returncode + + payload = { + "command": cmd, + "peak_rss_bytes": peak, + "peak_rss_mb": round(peak / (1024 * 1024), 3), + "returncode": rc, + "sample_count": len(samples), + "samples_tail": samples[-20:], + "wall_seconds": round(wall, 3), + } + output.write_text(json.dumps(payload, indent=2, sort_keys=True), encoding="utf-8") + return rc + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.stderr b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.stderr new file mode 100644 index 00000000..a1e26446 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.stderr @@ -0,0 +1 @@ +Error: analyze run a0fb3be2-c713-4805-80b2-07bd96e5a159 failed — InsertEntity for python:function:elspeth.core.landscape.execution_repository.ExecutionRepository.complete_node_state: sqlite error: UNIQUE constraint failed: entities.id diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.stdout b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.stdout new file mode 100644 index 00000000..3e058e3a --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.stdout @@ -0,0 +1,11 @@ +2026-05-18T00:19:08.063472Z  INFO discovered plugin plugin_id=python executable=/home/john/clarion/plugins/python/.venv/bin/clarion-plugin-python +2026-05-18T00:19:08.076379Z  INFO source tree walk complete file_count=1526 +2026-05-18T00:19:08.076602Z  INFO processing plugin plugin_id=python file_count=1526 +2026-05-18T00:26:52.543145Z  WARN plugin host collected findings plugin_id=python finding_count=6 +2026-05-18T00:26:52.543188Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.integration.cli.test_instantiate_plugins_value_source._build_yaml_with_model", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "0", "source_byte_end": "3309", "source_byte_start": "2425"} +2026-05-18T00:26:52.543198Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.integration.audit.test_pass_through_violation_persists.TestAuditRoundTrip.test_json_extract_returns_per_token_identifiers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "15", "source_byte_end": "6229", "source_byte_start": "5123"} +2026-05-18T00:26:52.543205Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.scripts.cicd.test_adr019_test_inventory.test_positive_fixture_reports_required_finding_kinds", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "1", "source_byte_end": "1642", "source_byte_start": "613"} +2026-05-18T00:26:52.543212Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "0", "source_byte_end": "277113", "source_byte_start": "275103"} +2026-05-18T00:26:52.543218Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "1", "source_byte_end": "276976", "source_byte_start": "275103"} +2026-05-18T00:26:52.543224Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "2", "source_byte_end": "276221", "source_byte_start": "275103"} +2026-05-18T00:26:56.106206Z ERROR writer-actor rejected insert; failing run plugin_id=python error=InsertEntity for python:function:elspeth.core.landscape.execution_repository.ExecutionRepository.complete_node_state diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.timing b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.timing new file mode 100644 index 00000000..160196ab --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/analyze.timing @@ -0,0 +1 @@ +EXIT=0 ELAPSED_SEC= diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0017Z/corpus-copy.txt b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/corpus-copy.txt new file mode 100644 index 00000000..ba8d756c --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/corpus-copy.txt @@ -0,0 +1,1532 @@ +/tmp/clarion-b8-elspeth-full-20260518T0016Z/tests/conftest.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/tests/__init__.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/codex_exemption_validator.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/check_contracts.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/codex_test_defect_hunt.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/codex_audit_common.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/generate_test_data.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/validate_deployment.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/run_mutation_testing.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/codex_integration_seam_hunt.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/generate_test_bugs.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/scripts/__init__.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/examples/chroma_rag/seed_collection.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/evals/__init__.py +/tmp/clarion-b8-elspeth-full-20260518T0016Z/examples/large_scale_test/generate_data.py 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b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/elspeth-dirty-status.txt @@ -0,0 +1,109 @@ + M AGENTS.md + M CLAUDE.md + M config/cicd/enforce_tier_model/plugins.yaml + M docs/composer/ux-redesign-2026-05/00-implementation-roadmap.md + M docs/composer/ux-redesign-2026-05/17-phase-5a-dynamic-source-from-chat.md + M docs/composer/ux-redesign-2026-05/18-phase-5b-surface-llm-interpretation.md + M docs/composer/ux-redesign-2026-05/18a-phase-5b-backend.md + M docs/composer/ux-redesign-2026-05/18b-phase-5b-frontend.md + M src/elspeth/engine/orchestrator/core.py + M src/elspeth/engine/orchestrator/export.py + M src/elspeth/plugins/infrastructure/base.py + M src/elspeth/plugins/sinks/azure_blob_sink.py + M src/elspeth/plugins/sinks/chroma_sink.py + M src/elspeth/plugins/sinks/csv_sink.py + M src/elspeth/plugins/sinks/database_sink.py + M src/elspeth/plugins/sinks/json_sink.py + M src/elspeth/plugins/sources/azure_blob_source.py + M src/elspeth/plugins/sources/csv_source.py + M src/elspeth/plugins/sources/json_source.py + M src/elspeth/plugins/sources/text_source.py + M src/elspeth/plugins/transforms/azure/content_safety.py + M src/elspeth/plugins/transforms/azure/prompt_shield.py + M src/elspeth/plugins/transforms/batch_classifier_metrics.py + M src/elspeth/plugins/transforms/batch_data_quality_report.py + M src/elspeth/plugins/transforms/batch_distribution_profile.py + M src/elspeth/plugins/transforms/batch_drift_compare.py + M src/elspeth/plugins/transforms/batch_effect_size.py + M src/elspeth/plugins/transforms/batch_experiment_compare.py + M src/elspeth/plugins/transforms/batch_outlier_annotator.py + M src/elspeth/plugins/transforms/batch_paired_preference.py + M src/elspeth/plugins/transforms/batch_replicate.py + M src/elspeth/plugins/transforms/batch_stats.py + M src/elspeth/plugins/transforms/batch_threshold_summary.py + M src/elspeth/plugins/transforms/batch_top_k.py + M src/elspeth/plugins/transforms/field_mapper.py + M src/elspeth/plugins/transforms/json_explode.py + M src/elspeth/plugins/transforms/line_explode.py + M src/elspeth/plugins/transforms/passthrough.py + M src/elspeth/plugins/transforms/report_assemble.py + M src/elspeth/plugins/transforms/truncate.py + M src/elspeth/plugins/transforms/type_coerce.py + M src/elspeth/plugins/transforms/value_transform.py + M src/elspeth/web/sessions/routes.py + M tests/e2e/audit/test_attributability.py + M tests/e2e/audit/test_full_lineage.py + M tests/fixtures/base_classes.py + M tests/fixtures/pipeline.py + M tests/fixtures/plugins.py + M tests/integration/_adr019_test_plugins.py + M tests/integration/audit/test_can_drop_rows_roundtrip.py + M tests/integration/audit/test_recorder_explain.py + M tests/integration/audit/test_sink_required_fields_serialization_roundtrip.py + M tests/integration/audit/test_source_guaranteed_fields_serialization_roundtrip.py + M tests/integration/config/test_schema_validation_integration.py + M tests/integration/pipeline/orchestrator/test_branch_transforms.py + M tests/integration/pipeline/orchestrator/test_declaration_contract_aggregate.py + M tests/integration/pipeline/orchestrator/test_execution_loop.py + M tests/integration/pipeline/orchestrator/test_gate_to_gate_routing.py + M tests/integration/pipeline/orchestrator/test_graceful_shutdown.py + M tests/integration/pipeline/orchestrator/test_orchestrator_cleanup.py + M tests/integration/pipeline/orchestrator/test_orchestrator_core.py + M tests/integration/pipeline/orchestrator/test_pass_through_flush.py + M tests/integration/pipeline/orchestrator/test_t18_characterization.py + M tests/integration/pipeline/test_aggregation_checkpoint_bug.py + M tests/integration/pipeline/test_composer_runtime_agreement.py + M tests/integration/pipeline/test_explicit_sink_routing.py + M tests/integration/pipeline/test_resume_comprehensive.py + M tests/integration/pipeline/test_retry.py + M tests/integration/rate_limit/test_integration.py + M tests/integration/telemetry/test_wiring.py + M tests/invariants/test_harness_self_test.py + M tests/invariants/test_pass_through_invariants.py + M tests/property/audit/test_fork_coalesce_flow.py + M tests/property/audit/test_terminal_states.py + M tests/property/core/test_dag_step_map_properties.py + M tests/property/engine/test_processor_properties.py + M tests/unit/contracts/test_plugin_roles.py + M tests/unit/contracts/test_telemetry_contracts.py + M tests/unit/contracts/transform_contracts/test_batch_transform_protocol.py + M tests/unit/core/dag/test_output_schema_enforcement.py + M tests/unit/core/landscape/test_run_lifecycle_repository.py + M tests/unit/core/landscape/test_schema.py + M tests/unit/core/test_explicit_sink_routing_safeguards.py + M tests/unit/core/test_token_outcomes.py + M tests/unit/engine/orchestrator/test_phase_error_masking.py + M tests/unit/engine/test_declared_required_fields_contract.py + M tests/unit/engine/test_schema_config_mode_contract.py + M tests/unit/engine/test_sink_required_fields_contract.py + M tests/unit/engine/test_source_guaranteed_fields_contract.py + M tests/unit/plugins/batching/test_batch_transform_mixin.py + M tests/unit/plugins/infrastructure/test_base_semantics.py + M tests/unit/plugins/infrastructure/test_divert_row.py + M tests/unit/plugins/llm/test_plugin_registration.py + M tests/unit/plugins/sinks/test_csv_sink.py + M tests/unit/plugins/sinks/test_database_sink.py + M tests/unit/plugins/sinks/test_json_sink.py + M tests/unit/plugins/sources/test_declared_guaranteed_fields.py + M tests/unit/plugins/sources/test_null_source.py + M tests/unit/plugins/test_base.py + M tests/unit/plugins/test_base_sink.py + M tests/unit/plugins/test_base_sink_contract.py + M tests/unit/plugins/test_base_source_contract.py + M tests/unit/plugins/test_integration.py + M tests/unit/plugins/test_invariant_probe_execution.py + M tests/unit/plugins/test_node_id_protocol.py + M tests/unit/plugins/test_protocols.py + M tests/unit/web/composer/test_compose_loop_envelope.py +?? docs/superpowers/plans/2026-05-18-report-assemble-aggregation.md +?? tests/unit/plugins/infrastructure/test_determinism_declaration_contract.py diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0017Z/extract-db-metrics.py b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/extract-db-metrics.py new file mode 100644 index 00000000..9be0b353 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0017Z/extract-db-metrics.py @@ -0,0 +1,116 @@ +#!/usr/bin/env python3 +"""Extract analyze-time measurements from clarion.db for the B.8 memo.""" + +from __future__ import annotations + +import json +import sqlite3 +import sys +from collections import Counter +from pathlib import Path + + +def main() -> int: + if len(sys.argv) != 3: + print("usage: extract-metrics.py ") + return 2 + db_path = Path(sys.argv[1]) + out_path = Path(sys.argv[2]) + + conn = sqlite3.connect(db_path) + conn.row_factory = sqlite3.Row + + payload: dict = {} + + # Tables present + payload["tables"] = sorted( + row[0] for row in conn.execute( + "SELECT name FROM sqlite_master WHERE type='table'" + ) + ) + + def table_count(name: str) -> int | None: + if name not in payload["tables"]: + return None + return conn.execute(f"SELECT COUNT(*) FROM {name}").fetchone()[0] + + payload["entities_total"] = table_count("entities") + payload["edges_total"] = table_count("edges") + payload["findings_total"] = table_count("findings") + payload["runs_total"] = table_count("runs") + + if "entities" in payload["tables"]: + payload["entities_by_kind"] = { + row["kind"]: row["c"] + for row in conn.execute( + "SELECT kind, COUNT(*) AS c FROM entities GROUP BY kind ORDER BY kind" + ) + } + + if "edges" in payload["tables"]: + payload["edges_by_kind_confidence"] = [ + {"kind": row["kind"], "confidence": row["confidence"], "count": row["c"]} + for row in conn.execute( + "SELECT kind, confidence, COUNT(*) AS c " + "FROM edges GROUP BY kind, confidence ORDER BY kind, confidence" + ) + ] + + # Runs table — most recent run details + if "runs" in payload["tables"]: + cols = [r[1] for r in conn.execute("PRAGMA table_info(runs)")] + payload["runs_columns"] = cols + rows = list(conn.execute("SELECT * FROM runs ORDER BY rowid DESC LIMIT 5")) + payload["recent_runs"] = [dict(r) for r in rows] + + # Findings breakdown + if "findings" in payload["tables"]: + finding_cols = [r[1] for r in conn.execute("PRAGMA table_info(findings)")] + payload["findings_columns"] = finding_cols + if "code" in finding_cols: + payload["findings_by_code"] = { + row["code"]: row["c"] + for row in conn.execute( + "SELECT code, COUNT(*) AS c FROM findings GROUP BY code ORDER BY code" + ) + } + + # Run stats (counters embedded in runs.stats JSON if present) + if "runs" in payload["tables"] and "stats" in ( + r[1] for r in conn.execute("PRAGMA table_info(runs)") + ): + stats_row = conn.execute( + "SELECT stats FROM runs ORDER BY rowid DESC LIMIT 1" + ).fetchone() + if stats_row and stats_row[0]: + try: + payload["latest_run_stats"] = json.loads(stats_row[0]) + except json.JSONDecodeError: + payload["latest_run_stats_raw"] = stats_row[0] + + # Unresolved-call-site side table if present + for side_table in ( + "entity_unresolved_call_sites", + "unresolved_call_sites", + "unresolved_reference_sites", + ): + if side_table in payload["tables"]: + payload[f"{side_table}_rows"] = conn.execute( + f"SELECT COUNT(*) FROM {side_table}" + ).fetchone()[0] + + # DB file size + payload["db_file_bytes"] = db_path.stat().st_size + + out_path.write_text(json.dumps(payload, indent=2, sort_keys=True, default=str), encoding="utf-8") + print(json.dumps({ + "wall_db_bytes": payload["db_file_bytes"], + "entities_total": payload["entities_total"], + "edges_total": payload["edges_total"], + "tables": payload["tables"], + }, indent=2)) + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-metrics.json b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-metrics.json new file mode 100644 index 00000000..fbaea5d9 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-metrics.json @@ -0,0 +1,94 @@ +{ + "command": [ + "/home/john/clarion/target/release/clarion", + "analyze", + "/tmp/clarion-b8-elspeth-full-20260518T0016Z" + ], + "peak_rss_bytes": 197865472, + "peak_rss_mb": 188.699, + "returncode": 0, + "sample_count": 1938, + "samples_tail": [ + { + "rss_bytes": 197865472, + "t": 479.897 + }, + { + "rss_bytes": 197865472, + "t": 480.147 + }, + { + "rss_bytes": 197865472, + "t": 480.397 + }, + { + "rss_bytes": 182169600, + "t": 480.648 + }, + { + "rss_bytes": 182169600, + "t": 480.898 + }, + { + "rss_bytes": 182169600, + "t": 481.148 + }, + { + "rss_bytes": 182169600, + "t": 481.398 + }, + { + "rss_bytes": 180731904, + "t": 481.648 + }, + { + "rss_bytes": 180731904, + "t": 481.898 + }, + { + "rss_bytes": 180731904, + "t": 482.149 + }, + { + "rss_bytes": 180731904, + "t": 482.399 + }, + { + "rss_bytes": 180731904, + "t": 482.649 + }, + { + "rss_bytes": 180731904, + "t": 482.899 + }, + { + "rss_bytes": 180731904, + "t": 483.149 + }, + { + "rss_bytes": 180731904, + "t": 483.4 + }, + { + "rss_bytes": 180731904, + "t": 483.65 + }, + { + "rss_bytes": 180731904, + "t": 483.9 + }, + { + "rss_bytes": 180731904, + "t": 484.15 + }, + { + "rss_bytes": 180731904, + "t": 484.4 + }, + { + "rss_bytes": 0, + "t": 484.651 + } + ], + "wall_seconds": 484.651 +} \ No newline at end of file diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-with-rss.py b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-with-rss.py new file mode 100644 index 00000000..e44df106 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-with-rss.py @@ -0,0 +1,95 @@ +#!/usr/bin/env python3 +"""Run clarion analyze and sample peak RSS for B.8 measurement. + +Mirrors the analyze-metrics.json schema from the 2026-05-17 B.8 run. +""" + +from __future__ import annotations + +import json +import os +import subprocess +import sys +import time +from pathlib import Path + + +def _rss_bytes_for_tree(root_pid: int) -> int: + """Sum VmRSS across the process and its descendants.""" + pids = [root_pid] + try: + with open(f"/proc/{root_pid}/task/{root_pid}/children", "r") as fh: + for child_pid in fh.read().split(): + pids.append(int(child_pid)) + except FileNotFoundError: + pass + # one more level for plugin grandchildren (pyright etc.) + expanded = list(pids) + for pid in pids[1:]: + try: + with open(f"/proc/{pid}/task/{pid}/children", "r") as fh: + for child_pid in fh.read().split(): + expanded.append(int(child_pid)) + except FileNotFoundError: + pass + total = 0 + for pid in expanded: + try: + with open(f"/proc/{pid}/status", "r") as fh: + for line in fh: + if line.startswith("VmRSS:"): + kib = int(line.split()[1]) + total += kib * 1024 + break + except FileNotFoundError: + continue + return total + + +def main() -> int: + if len(sys.argv) < 3: + print("usage: analyze-with-rss.py [args...]") + return 2 + output = Path(sys.argv[1]) + cmd = sys.argv[2:] + + env = os.environ.copy() + plugin_bin_dir = "/home/john/clarion/plugins/python/.venv/bin" + env["PATH"] = plugin_bin_dir + ":" + env.get("PATH", "") + + start = time.monotonic() + proc = subprocess.Popen(cmd, env=env) + samples: list[dict[str, float | int]] = [] + peak = 0 + try: + while True: + ret = proc.poll() + now = time.monotonic() - start + rss = _rss_bytes_for_tree(proc.pid) + samples.append({"t": round(now, 3), "rss_bytes": rss}) + if rss > peak: + peak = rss + if ret is not None: + break + time.sleep(0.25) + except KeyboardInterrupt: + proc.terminate() + raise + wall = time.monotonic() - start + rc = proc.returncode + + payload = { + "command": cmd, + "peak_rss_bytes": peak, + "peak_rss_mb": round(peak / (1024 * 1024), 3), + "returncode": rc, + "sample_count": len(samples), + "samples_tail": samples[-20:], + "wall_seconds": round(wall, 3), + } + output.write_text(json.dumps(payload, indent=2, sort_keys=True), encoding="utf-8") + return rc + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.stderr b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.stderr new file mode 100644 index 00000000..e69de29b diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.stdout b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.stdout new file mode 100644 index 00000000..8f12b1f7 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.stdout @@ -0,0 +1,12 @@ +2026-05-18T01:51:06.155391Z  INFO discovered plugin plugin_id=python executable=/home/john/clarion/plugins/python/.venv/bin/clarion-plugin-python +2026-05-18T01:51:06.168911Z  INFO source tree walk complete file_count=1526 +2026-05-18T01:51:06.169049Z  INFO processing plugin plugin_id=python file_count=1526 +2026-05-18T01:59:03.194694Z  WARN plugin host collected findings plugin_id=python finding_count=6 +2026-05-18T01:59:03.194720Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.integration.cli.test_instantiate_plugins_value_source._build_yaml_with_model", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "0", "source_byte_end": "3309", "source_byte_start": "2425"} +2026-05-18T01:59:03.194730Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.integration.audit.test_pass_through_violation_persists.TestAuditRoundTrip.test_json_extract_returns_per_token_identifiers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "15", "source_byte_end": "6229", "source_byte_start": "5123"} +2026-05-18T01:59:03.194738Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.scripts.cicd.test_adr019_test_inventory.test_positive_fixture_reports_required_finding_kinds", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "1", "source_byte_end": "1642", "source_byte_start": "613"} +2026-05-18T01:59:03.194745Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "0", "source_byte_end": "277113", "source_byte_start": "275103"} +2026-05-18T01:59:03.194751Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "1", "source_byte_end": "276976", "source_byte_start": "275103"} +2026-05-18T01:59:03.194757Z  WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.unit.web.composer.test_tools.TestPreviewPipeline.test_preview_pipeline_suggests_fork_gate_for_duplicate_consumers", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "2", "source_byte_end": "276221", "source_byte_start": "275103"} +2026-05-18T01:59:10.585548Z  INFO plugin complete plugin_id=python entity_count=33250 edge_count=93963 +analyze complete: run 3461ded9-5ba9-4b44-9f28-dd7dab7028d4 completed (33250 entities, 93963 edges) diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.timing b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.timing new file mode 100644 index 00000000..49d5cfc1 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze.timing @@ -0,0 +1 @@ +EXIT=0 diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/elspeth-commit.txt b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/elspeth-commit.txt new file mode 100644 index 00000000..5f1fc963 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/elspeth-commit.txt @@ -0,0 +1 @@ +9d3fd55d63bac764c88af04330af2c3f4f651346 diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-live.stderr b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-live.stderr new file mode 100644 index 00000000..e69de29b diff --git a/tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-output-live.json b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-output-live.json new file mode 100644 index 00000000..abc3811b --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T0114Z/mcp-driver-output-live.json @@ -0,0 +1,3849 @@ +{ + "clarion_bin": "/home/john/clarion/target/release/clarion", + "config": "/tmp/clarion-b8-elspeth-full-20260518T0016Z/clarion-b8-live.yaml", + "generated_at_unix": 1779071021, + "initialize": { + "id": "init", + "jsonrpc": "2.0", + "result": { + "capabilities": { + "tools": {} + }, + "protocolVersion": "2025-11-25", + "serverInfo": { + "name": "clarion", + "version": "0.1.0-dev" + } + } + }, + "initialize_latency_ms": 6.269, + "manifest": [ + { + "arguments": { 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processing plugin plugin_id=python file_count=1526 +2026-05-18T11:54:15.353451Z WARN plugin host collected findings plugin_id=python finding_count=6 +2026-05-18T11:54:15.353483Z WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.integration.cli.test_instantiate_plugins_value_source._build_yaml_with_model", "reason": "callee_expr exceeds 512 bytes", "site_ordinal": "0", "source_byte_end": "3309", "source_byte_start": "2425"} +2026-05-18T11:54:15.353492Z WARN plugin host finding plugin_id=python subcode=CLA-INFRA-PLUGIN-MALFORMED-UNRESOLVED-CALL-SITE plugin emitted malformed unresolved call site: callee_expr exceeds 512 bytes metadata={"caller_entity_id": "python:function:tests.integration.audit.test_pass_through_violation_persists.TestAuditRoundTrip.test_json_extract_returns_per_token_identifiers", "reason": 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bytes", "site_ordinal": "2", "source_byte_end": "276221", "source_byte_start": "275103"} +2026-05-18T11:54:23.822339Z INFO plugin complete plugin_id=python entity_count=33250 edge_count=107568 +2026-05-18T11:54:24.104686Z INFO phase3 emitted weak-modularity finding run_id=5bfeacdd-b93e-4a02-b974-978c3d645bb2 +analyze complete: run 5bfeacdd-b93e-4a02-b974-978c3d645bb2 completed (33350 entities, 108690 edges) diff --git a/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/clustering-stats.json b/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/clustering-stats.json new file mode 100644 index 00000000..8c5dc56f --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/clustering-stats.json @@ -0,0 +1 @@ +{"algorithm":"leiden","duration_ms":280,"edge_types":["imports","calls"],"enabled":true,"in_subsystem_edges_inserted":1122,"max_iterations":100,"min_cluster_size":3,"modularity_score":0.020884003737243844,"module_count":1526,"module_edge_count":7217,"resolution":1.0,"seed":42,"skipped_reason":null,"status":"completed","subsystem_count":100,"subsystems_inserted":100,"weak_modularity_finding_emitted":true,"weak_modularity_threshold":0.3,"weight_by":"reference_count"} diff --git a/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/corpus-provenance.md b/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/corpus-provenance.md new file mode 100644 index 00000000..45dd22d9 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/corpus-provenance.md @@ -0,0 +1,28 @@ +# Phase 3 Corpus Provenance + +The 2026-05-18T1138Z Phase 3 perf run used the B.8 elspeth corpus at: + +```text +/tmp/clarion-b8-elspeth-full-20260518T0016Z +``` + +That temporary directory is not committed. The committed provenance from the +corpus creation pass is: + +- elspeth commit: `9d3fd55d63bac764c88af04330af2c3f4f651346` +- copied file manifest: `tests/perf/b8_scale_test/results/2026-05-18T0017Z/corpus-copy.txt` +- dirty status: `tests/perf/b8_scale_test/results/2026-05-18T0017Z/elspeth-dirty-status.txt` + +To re-derive a comparable corpus from an elspeth checkout, run. The script +copies Python files reported by `git ls-files -co --exclude-standard '*.py'`, +so it includes tracked and non-ignored untracked source files without pulling in +ignored virtualenv or frontend dependency trees. + +```bash +bash tests/perf/b8_scale_test/derive-elspeth-corpus.sh \ + /path/to/elspeth \ + /tmp/clarion-b8-elspeth-corpus-$(date -u +%Y%m%dT%H%M%SZ) +``` + +Then use the emitted output directory as the `clarion install --path` and +`clarion analyze` target. diff --git a/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/phase3-results.md b/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/phase3-results.md new file mode 100644 index 00000000..34c84465 --- /dev/null +++ b/tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/phase3-results.md @@ -0,0 +1,49 @@ +# Phase 3 Clustering Performance Result + +Date: 2026-05-18 + +Corpus: `/tmp/clarion-b8-elspeth-full-20260518T0016Z` + +Reproducibility status: directional historical measurement. The temporary +corpus path is not committed; see `corpus-provenance.md` and +`tests/perf/b8_scale_test/derive-elspeth-corpus.sh` for the committed procedure +to re-derive a comparable corpus from an elspeth checkout. + +Command: + +```bash +corpus_dir=$(bash tests/perf/b8_scale_test/derive-elspeth-corpus.sh \ + /path/to/elspeth \ + /tmp/clarion-b8-elspeth-corpus-$(date -u +%Y%m%dT%H%M%SZ)) +target/release/clarion install --force --path "$corpus_dir" +python3 tests/perf/b8_scale_test/results/2026-05-18T0114Z/analyze-with-rss.py \ + tests/perf/b8_scale_test/results/2026-05-18T1138Z-phase3/analyze-metrics.json \ + /home/john/clarion/target/release/clarion analyze \ + "$corpus_dir" +``` + +Baseline from `2026-05-18T0114Z`: + +- Wall time: 484.651s +- Peak RSS: 188.699 MiB + +Phase 3 run: + +- Wall time: 377.811s +- Peak RSS: 198.098 MiB +- `runs.stats.clustering.duration_ms`: 280ms +- Module count: 1,526 +- Module dependency edges: 7,217 +- Subsystems inserted: 100 +- `in_subsystem` edges inserted: 1,122 + +Acceptance: + +- Wall-time overhead: PASS. Phase 3 measured clustering duration is 0.280s, + below the 60s limit. +- RSS overhead: PASS. Whole-run peak RSS is +9.399 MiB relative to the B.8 + baseline, below the 500 MiB limit. + +The run emitted `CLA-FACT-CLUSTERING-WEAK-MODULARITY` because the full elspeth +graph modularity score was 0.020884003737243844, below the v0.1 threshold of +0.3. diff --git a/tests/perf/b8_scale_test/test_driver.py b/tests/perf/b8_scale_test/test_driver.py new file mode 100644 index 00000000..5fd74dbd --- /dev/null +++ b/tests/perf/b8_scale_test/test_driver.py @@ -0,0 +1,227 @@ +import json +import sys +from pathlib import Path + +import pytest + +sys.path.insert(0, str(Path(__file__).parent)) + +import driver # noqa: E402 + + +def test_percentile_uses_nearest_rank_for_tail_latency() -> None: + values = [100.0, 20.0, 40.0, 10.0] + + assert driver.percentile(values, 50) == 40.0 + assert driver.percentile(values, 95) == 100.0 + assert driver.percentile([], 95) is None + + +def test_parse_tool_response_extracts_envelope_and_size() -> None: + envelope = { + "ok": True, + "result": {"cache": {"hit": True}}, + "error": None, + "truncated": False, + "stats_delta": {"summary_cache_hits_total": 1}, + } + response = { + "jsonrpc": "2.0", + "id": "summary-1", + "result": {"content": [{"type": "text", "text": json.dumps(envelope)}]}, + } + + parsed = driver.parse_tool_response( + "medium-warm", + "summary", + "steady_state", + "warm", + response, + 125.0, + 512, + ) + + assert parsed.pattern == "medium-warm" + assert parsed.tool == "summary" + assert parsed.phase == "steady_state" + assert parsed.cache_state == "warm" + assert parsed.ok is True + assert parsed.unavailable is False + assert parsed.cache_hit is True + assert parsed.estimated_response_tokens == 128 + assert parsed.stats_delta == {"summary_cache_hits_total": 1} + assert parsed.response_bytes == 512 + + +def test_summarize_records_groups_by_pattern_and_tool() -> None: + records = [ + driver.CallRecord( + "light", + "find_entity", + "steady_state", + "none", + 20.0, + 100, + 25, + True, + False, + False, + True, + None, + None, + {}, + ), + driver.CallRecord( + "light", + "find_entity", + "steady_state", + "none", + 40.0, + 120, + 30, + True, + False, + False, + True, + None, + None, + {}, + ), + driver.CallRecord( + "light", + "summary", + "warmup", + "cold", + 100.0, + 200, + 50, + True, + False, + False, + True, + True, + None, + {"summary_tokens_total": 5}, + ), + driver.CallRecord( + "light", + "callers_of", + "steady_state", + "inferred", + 150.0, + 220, + 55, + False, + True, + False, + False, + None, + None, + {"inferred_tokens_total": 7, "inferred_cost_usd": 0.002}, + ), + driver.CallRecord( + "light", + "summary", + "steady_state", + "warm", + 180.0, + 220, + 55, + False, + True, + False, + False, + None, + None, + {"summary_tokens_total": 3, "summary_cost_usd": 0.001}, + ), + driver.CallRecord( + "light", + "summary", + "steady_state", + "warm", + 300.0, + 240, + 60, + True, + False, + True, + False, + False, + "llm-disabled", + {}, + ), + ] + + summary = driver.summarize_records(records) + + find = summary["by_pattern"]["light"]["tools"]["find_entity"] + assert find["call_count"] == 2 + assert find["p50_latency_ms"] == 40.0 + assert find["p95_latency_ms"] == 40.0 + assert find["response_size_p95_kb"] == pytest.approx(0.117, abs=0.001) + assert find["response_tokens_p95"] == 30 + assert find["useful_result_count"] == 2 + + pattern = summary["by_pattern"]["light"] + assert pattern["call_count"] == 6 + assert pattern["unavailable_count"] == 1 + assert pattern["summary_cache_hit_rate"] == 0.5 + assert pattern["tokens_total"] == 15 + assert pattern["cost_usd"] == pytest.approx(0.003, abs=0.0001) + assert summary["by_phase"]["steady_state"]["call_count"] == 5 + assert summary["gate"]["steady_state_storage_backed"]["p95_latency_ms"] == 150.0 + assert driver.summary_miss_then_hit(records) is False + + +def test_manifest_is_deterministic_and_marks_cache_state() -> None: + targets = driver.QueryTargets( + entity_at=[{"id": "e0", "file": "demo.py", "line": 1}], + find_patterns=["demo"], + caller_targets=["target"], + path_roots=["entry"], + summary_ids=["summary"], + issues_ids=["issues"], + neighborhood_ids=["neighbor"], + inferred_targets=["inferred"], + ) + + requests, skipped = driver.build_requests( + targets, heavy_count=50, include_inferred=True + ) + + assert skipped == [] + assert [(request.label, request.tool) for request in requests[:5]] == [ + ("L01-entity-at", "entity_at"), + ("L02-find-entity", "find_entity"), + ("L03-callers-of", "callers_of"), + ("L04-neighborhood", "neighborhood"), + ("L05-entity-at-repeat", "entity_at"), + ] + medium_summary = [ + request + for request in requests + if request.pattern == "medium-cold" and request.tool == "summary" + ] + assert len(medium_summary) == 3 + assert {request.phase for request in medium_summary} == {"warmup"} + assert {request.cache_state for request in medium_summary} == {"cold"} + + warm_summary = [ + request + for request in requests + if request.pattern == "medium-warm" and request.tool == "summary" + ] + assert len(warm_summary) == 3 + assert {request.arguments["id"] for request in warm_summary} == {"summary"} + assert {request.cache_state for request in warm_summary} == {"warm"} + + heavy_summary = [ + request + for request in requests + if request.pattern == "heavy" and request.tool == "summary" + ] + assert heavy_summary + assert {request.phase for request in heavy_summary} == {"steady_state"} + assert {request.cache_state for request in heavy_summary} == {"warm"} + assert heavy_summary[0].label.startswith("H")