Align public repo with Runtime, Protocol, and Proof boundary

[squaeragent]

Summary

Align the public zero-intel/zero repository with the v95 Runtime / Protocol / Proof boundary.

This keeps the public repo focused on the open substrate while leaving hosted product surfaces outside this repository:

• ZERO Runtime, ZERO Protocol, ZERO Proof, CLI, and developer verification stay in this repo.
• Hosted ZERO Studio, ZERO Control, ZERO Registry, app, founder/admin, and doctrine/design-system surfaces are explicitly out of public repo scope.
• Stale Network / Intelligence / Engine public-surface framing is updated or demoted to historical/internal context.
• Historical roadmap/audit documents now carry status disclaimers so they are not mistaken for current product IA.
• Generated LLM context freshness is now part of the public readiness gate.

Safety

• Docs, metadata, generated context, and gate checks only.
• No Runtime/live/trading behavior changes.
• No secrets, env vars, VPS state, database, or deployment changes.

Verification

• scripts/generate_llms_full.py
• just stale-artifact-check
• just docs-check
• just public-readiness
• just hardening-gate
• just public-proof
• git diff --check
• cd cli && cargo metadata --no-deps --format-version 1 >/tmp/zero-public-cargo-metadata.json && python3 -m json.tool /tmp/zero-public-cargo-metadata.json >/dev/null
• TOML parse for engine/pyproject.toml and cli/Cargo.toml

Summary by CodeRabbit

• Documentation

  • Clarified ZERO as an open Runtime, Protocol, and Proof substrate and refined public-repo boundary language
  • Rewrote several docs to emphasize which product surfaces are external, renamed linked plans/audits (historical/autonomy and runtime capability boundary), and adjusted evolution/commercial framing

• Chores

  • Updated package metadata/keywords and project description to match positioning
  • Strengthened public-readiness verification to include expanded content checks and an additional documentation generation check

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: f03db456-f992-4421-a5d7-a04f20cf8c1b

📥 Commits

Reviewing files that changed from the base of the PR and between 3fb620b and 2c13046.

📒 Files selected for processing (3)

• README.md
• docs/llms-full.txt
• docs/positioning.md

📝 Walkthrough

Walkthrough

This PR updates public-facing copy and generated docs to present ZERO as an open Runtime, Protocol, and Proof substrate and clarifies that hosted product surfaces (Studio, Control, Registry, etc.) are external to the repository; it also updates LLM context generation, readiness checks, and some package metadata.

Changes

ZERO Public Boundary & Product Positioning

Layer / File(s)	Summary
Product positioning and README updates README.md, docs/positioning.md, docs/llms.txt, llms.txt	Reframed README and positioning text to emphasize "open Runtime, Protocol, and Proof substrate", replaced "Product Surfaces" with "Open Repository Surfaces", standardized "Runtime control packet" wording, renamed linked docs to "Historical Autonomous OS Plan" and "Runtime Capability Boundary Audit", and clarified hosted surfaces are external.
Architecture and boundary documentation alignment docs/architecture.md, docs/open-core-boundary.md, docs/autonomous-os-plan.md, docs/private-engine-capability-gap-audit.md, docs/public-upgrade.md	Rewrote architecture and boundary docs to define four first-class open surfaces (Runtime, Protocol, Proof, Developers), renamed "Public Engine Flow"→"Public Runtime Flow", reframed commercial flow to "ZERO Proof", and added historical/extraction status notes while explicitly excluding hosted Studio/Control/Registry surfaces from the repo.
Generated LLM documentation context docs/llms-full.txt	Updated generated LLM context excerpts to embed the refreshed README/architecture/boundary language, update the Open Repository Surfaces section, adjust the self-evolution loop references, and rename linked documentation entries across the embedded index.
Public readiness gate enforcement and metadata updates scripts/public_readiness_gate.sh, cli/Cargo.toml, engine/pyproject.toml	Added a generated-LLM-context check (generate_llms_full.py --check) to the readiness gate and expanded file_contains assertions to require updated public-facing phrases. Updated CLI workspace keywords and engine project description metadata to align terminology.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• zero-intel/zero#42: Shares updates to scripts/public_readiness_gate.sh assertions and LLM-doc generation checks enforcing renamed surface terms.
• zero-intel/zero#41: Overlapping documentation refactor adjusting Runtime/Protocol/Proof public-repo alignment and README/docs terminology.

Poem

🐰 New words on every page I sweep,
Runtime, Protocol, Proof — the fields we keep.
Docs aligned, the gate now sees,
Open surfaces on the breeze.
A little hop for clarity's leap.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title accurately reflects the main change across all files—aligning the public repository documentation and metadata with the Runtime, Protocol, and Proof boundary by updating positioning language and excluding hosted product surfaces.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/public-runtime-protocol-proof-docs

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[coderabbitai]

Actionable comments posted: 2

🧹 Nitpick comments (1)

README.md (1)

88-89: ⚡ Quick win

Clarify "legacy CLI language" reference.

The text describes /cockpit-mode as "legacy CLI language" but this is the current documented command with no alternative mentioned. This phrasing may confuse users into thinking the feature is deprecated when it appears to be the primary interface for accessing the Runtime control packet.

Consider either:

• Removing the "legacy" qualifier if the command naming is current
• Explaining what makes it "legacy" and what the preferred terminology is
• Clarifying that only the naming is legacy while the feature remains primary

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@README.md` around lines 88 - 89, The phrasing that calls "/cockpit-mode"
"legacy CLI language" is ambiguous; update the README text around "Runtime
control packet" and "/cockpit-mode" to either (a) remove the word "legacy" if
the command is current, (b) explicitly state what makes the naming legacy and
provide the preferred term, or (c) clarify that only the naming is legacy while
the feature remains primary—also mention "paper/default mode" behavior (refuse
live risk and show the reason) remains unchanged so readers understand the
command status versus functionality.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@docs/positioning.md`:
- Around line 57-74: Choose whether the repo defines four surfaces (ZERO
Runtime, ZERO Protocol, ZERO Proof, Developers with ZERO CLI treated as Runtime
tooling) or five distinct surfaces (adding ZERO CLI as its own surface and
possibly Evolution); then update the surface enumeration and wording
consistently in the docs by: adjusting the list items and headings for "ZERO
Runtime", "ZERO Protocol", "ZERO Proof", "ZERO CLI", and
"Developers"/"Evolution" wherever they appear; make the README table rows match
the chosen set and rephrase the sentence in the architecture doc that currently
says "four first-class open surfaces" so it matches the chosen count; ensure any
references to "CLI as tooling" or "Evolution as Runtime subsystem" are aligned
with the final decision.

---

Nitpick comments:
In `@README.md`:
- Around line 88-89: The phrasing that calls "/cockpit-mode" "legacy CLI
language" is ambiguous; update the README text around "Runtime control packet"
and "/cockpit-mode" to either (a) remove the word "legacy" if the command is
current, (b) explicitly state what makes the naming legacy and provide the
preferred term, or (c) clarify that only the naming is legacy while the feature
remains primary—also mention "paper/default mode" behavior (refuse live risk and
show the reason) remains unchanged so readers understand the command status
versus functionality.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 3fde8cc2-4ab1-4537-a5c1-d4b4cd734911

📥 Commits

Reviewing files that changed from the base of the PR and between 2dcae2d and 7a27be2.

📒 Files selected for processing (13)

• README.md
• cli/Cargo.toml
• docs/architecture.md
• docs/autonomous-os-plan.md
• docs/llms-full.txt
• docs/llms.txt
• docs/open-core-boundary.md
• docs/positioning.md
• docs/private-engine-capability-gap-audit.md
• docs/public-upgrade.md
• engine/pyproject.toml
• llms.txt
• scripts/public_readiness_gate.sh