fix: Isolate Native PTC Readiness and Watchdog Phases

[danny-avila]

Summary

• keep ordinary native workspace commands available when optional selected-workspace PTC dependencies or copy-on-write preflight are unavailable
• give PTC staging and commit separate bounded watchdog budgets, using the protocol execution default when run_timeout is omitted
• add an acknowledged IPC commit barrier so pre-commit failures remain mutation-atomic while post-barrier failures retain quarantine protection

Closes #201.
Closes #202.
Closes #203.

Focused verification

• npm run build (packages/code)
• node --test dist/native-process.test.js dist/native-programmatic.test.js dist/native-process-child.test.js dist/native-sandbox.test.js dist/native-pool.test.js (100 passed)
• LIBRECHAT_CODE_LIVE_SRT_TESTS=1 node --test dist/native-programmatic-live.test.js (real macOS SRT; probe side effects blocked and commit executed once)
• git diff --check

Codegraph test selection was unavailable on this host, so focused tests were selected from the affected native process, programmatic executor, sandbox, and pool dependency boundaries.

[danny-avila]

@codex review

Please review the current PR head bd8b1cc. Confirm that this exact commit is the reviewed commit and ignore findings that apply only to earlier heads.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-14T19:50:43.588175Z	bbc2f8d	Manual request

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[chatgpt-codex-connector]

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

Reviewed commit: bd8b1cc131

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[danny-avila]

@codex review

Please review the current PR head bbc2f8d. This head rebases onto main after #206 and #207 and preserves trusted Bash/jq resolution while making PTC readiness lazy. Confirm that this exact commit is the reviewed commit and ignore findings that apply only to earlier heads.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Bravo.

Reviewed commit: bbc2f8d27e

ℹ️ About Codex in GitHub

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• 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".