fix(wp4): close phase3 subsystem follow-ups

.agents/skills/filigree-workflow/SKILL.md

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+---
+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 <issue-id>                            → read requirements and context
+filigree transitions <issue-id>                     → check valid status transitions
+filigree start-work <issue-id> --assignee <name>    → atomically claim + transition to in_progress
+[do the work, commit code]
+filigree close <issue-id> --reason="summary of what was done"
+```
+
+Or skip steps 1–3 entirely with `filigree start-next-work --assignee <name>` 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 <ids...> --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 <issue-id> --assignee <agent-name>     # specific issue
+filigree start-next-work --assignee <agent-name>           # 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 <issue-id> --assignee <agent-name>     # reserve only, no transition
+filigree claim-next --assignee <agent-name>
+```
+
+## 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 <blocker-id>
+filigree create-plan --file plan.json   # milestone/phase/step hierarchy
+```
+
+### Managing Dependencies
+
+```bash
+filigree add-dep <issue> <depends-on>     # A depends on B
+filigree remove-dep <issue> <depends-on>
+filigree blocked                          # show all blocked issues
+```
+
+### Context and Handoff
+
+```bash
+filigree add-comment <id> "what I found / what's left to do"
+filigree get-comments <id>                # read previous context
+filigree show <id>                        # 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 <id> --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 <blocked> <blocker>`
+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 <id>      # 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 <id>`, check blocked_by |
+| "Multiple agents need work" | `filigree start-next-work --assignee <name>` |
+| "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 <timestamp>` |
+| "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 |

.agents/skills/filigree-workflow/examples/sprint-plan.json

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+{
+  "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"]}
+      ]
+    }
+  ]
+}