Allow Codex commits in standalone repositories

[itsHabib]

Summary

Codex local runs could edit files in standalone repositories but could not commit because the sandbox left the repository's .git directory read-only. This adds the validated standalone Git metadata directory as an explicit writable root while preserving the linked-worktree and separate-git-dir boundaries.

What this adds

Standalone repository Git writes

• Allows the spawned Codex process to write a canonical, direct-child .git directory for an ordinary repository.
• Canonicalizes symlinked workdirs before repository discovery.
• Rejects symlinked .git paths without imposing case-sensitive path spelling.
• Preserves the existing linked-worktree metadata roots and separate-git-dir refusal.

Regression coverage

• Covers canonical standalone repositories, symlinked workdirs, symlink rejection, filesystem casing, linked worktrees, and separate-git-dir repositories.

Validation

• make check
• pnpm --filter @ship/codex-runner test — 99 tests passed
• Ubuntu and Windows CI at 21300c3920083f77e51f20cfea7e0e79624f3490
• Codex exact-head review found no major issues
• Minimal Codex sandbox probe: commit blocked before the writable-root change and succeeded when .git was admitted
• RoxIQ Gauntlet rehearsal gnt_20260827T230200Z_1c7dc381485baa99 completed pass/none with a Codex-created repair commit

[itsHabib]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 23f8fb58f3

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".

[itsHabib]

@codex review

[chatgpt-codex-connector]

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

Reviewed commit: 21300c3920

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".