fix(agent): restore project skill runtime hardening

[kojiwakayama]

Summary

• restores the two effectively lost project-runtime hardening commits and the complete six-commit fix(agent): harden project skill runtime boundaries #3248 tail
• makes project file discovery bounded and atomic, hardens skill metadata/policy/reference handling, and preserves hosted-runtime composition
• removes the unsafe legacy parser/API path in favor of strict extension-owned YAML parsing
• includes only narrow compatibility repairs required by the rebuilt parent stack

Recovery topology

This PR is intentionally stacked as:

#3247 -> #3264 -> #3265 -> this PR

The original #3248 could not be rebased safely because its ancestry contained feature-base merges that never reached main. This branch reconstructs the intended deltas on durable exact parents without carrying unrelated historical branch history.

Do not force-update a parent branch after a child PR has merged; rebase the remaining child instead.

Verification

• focused changed suites: 355 passed across 100 test steps, 0 failed
• deno task verify:quick
• full typecheck
• deno task lint:test-typecheck: 80 grandfathered files, 0 new
• dependency, module, extension, and core third-party boundary checks
• docs validation
• git diff --check

[kojiwakayama]

@codex review

[kojiwakayama]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 8b01324a89

ℹ️ About Codex in GitHub

Codex has been enabled to automatically review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

When you sign up for Codex through ChatGPT, Codex can also answer questions or update the PR, like "@codex address that feedback".

[kojiwakayama]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 488085ccff

ℹ️ About Codex in GitHub

Codex has been enabled to automatically review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

When you sign up for Codex through ChatGPT, Codex can also answer questions or update the PR, like "@codex address that feedback".

[kojiwakayama]

Rebased onto the current #3265 head and reconciled the recovered project-skill runtime without compatibility shims. The update preserves the strict hosted transport, extension-owned parsing, atomic discovery publication, confirmed project identity, bounded built-in file reads, and fail-closed skill policy enforcement.\n\nValidation at 5ad7544:\n- 401 affected tests + 101 nested steps passed\n- deno task verify:quick passed\n- git diff --check passed\n- merge-tree against the exact current base ca4a345 is clean\n- no unresolved review threads

[kojiwakayama]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 5ad75446a2

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[kojiwakayama]

Restacked onto #3265 head 9344f1f2c; this PR is now 6ad11ceb2. The only tree delta from the prior head is the inherited skill-policy test correction, reconciled without weakening the recovered runtime contract.

Validation:

• 403 affected tests / 207 nested steps: green
• deno task verify:quick: green

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 6ad11ceb2e

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[kojiwakayama]

Addressed all six review findings and resolved their threads. The public project-file transport is immutable and bounded, pagination rejects cycles, public filters and content limits are preserved, and reference-only Skill loads retain the active policy atomically. The complete changed-test surface and verify:quick pass on the final stacked head. @codex review

[kojiwakayama]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: f0f639b922

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[kojiwakayama]

@codex review

Restacked patch-identically onto final #3265 head c3588f0de8; exact #3266 head is e0c21a5702fc887af2cd29ec275ed78a88a49dc8. Range-diff marks all seventeen child patches equal. The final stack passes 91 focused tests / 48 nested steps and verify:quick.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: e0c21a5702

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[kojiwakayama]

@codex review

[kojiwakayama]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Nice work!

Reviewed commit: 59beedff34

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[kojiwakayama]

@codex review exact head 033b50f. Fresh merge-blocking review requested after restack onto #3265 head e6b7c6d. Commits 2-19 are range-diff identical; commit 1 preserves the parent private-validator fix while retaining the stronger bounded owned-identity implementation. Agent project/runtime suite passes 553 tests / 622 steps and verify:quick passes.

[chatgpt-codex-connector]

You have reached your Codex usage limits for code reviews. You can see your limits in the Codex usage dashboard.
To continue using code reviews, add credits to your account and enable them for code reviews in your settings.

[kojiwakayama]

@codex review 3252f9e

[chatgpt-codex-connector]

You have reached your Codex usage limits for code reviews. You can see your limits in the Codex usage dashboard.
To continue using code reviews, add credits to your account and enable them for code reviews in your settings.

[kojiwakayama]

Final restack head: 0814ac8 on #3265 c496b58. All 19 child commits are range-diff identical. Exact top-of-stack verify:quick passes; the unchanged runtime delta passes 553 tests / 622 steps. Mergeability is clean and there are no unresolved review threads.