verify-Codex-run-commit-vs-working-tree-before-closing

Verify Codex run commit vs working tree before closing

When to use

Use this after a Codex implementation run that claims:

• files were changed and committed
• a GitHub issue was commented/closed
• verification passed

Especially important when:

• the repo has many unrelated dirty files
• pre-commit or repo-specific hooks may reject some paths
• Codex reports that some changes were applied but not committed
• the issue was closed automatically by the worker

Why this skill exists

A Codex implementation run can successfully commit and close an issue while still leaving intended edits in the working tree. Observed failure mode:

• Codex edited the target files
• some files were blocked from commit by repo rules / hooks / file policies
• Codex still posted a success comment and closed the issue
• the uncommitted delta remained in the working tree

This means "issue closed" is not sufficient evidence that all intended changes landed.

Required checks

After the run finishes, do all of these before declaring success:

1. Inspect the commit Codex claims landed

git show --stat --name-only <commit>

2. Verify the commit landed in the intended checkout / branch, not just somewhere in the repo ecosystem

git rev-parse --show-toplevel
git branch --show-current
git branch --contains <commit>

• if you launched Codex from an isolated worktree, confirm the commit is actually on that worktree branch
• do not assume workdir= or prompt text was sufficient protection
• if the commit landed on another local branch / checkout (for example dirty main) treat the worker result as only partially integrated

3. Compare that file list against the files Codex claimed to have changed in its final summary

• look for any claimed files missing from the commit stat

4. Inspect current working tree for owned-path leftovers

git status --short

• look specifically for files owned by the executed issue
• ignore unrelated dirty files outside the issue's owned paths

5. If a claimed file is still modified after the run:

• read it and confirm whether the intended change is present only in the working tree
• decide whether to:
  • make a tiny fixup commit, or
  • reopen the issue and finish properly

6. Verify GitHub closeout state

• read the latest issue comments
• check whether the issue is open/closed
• if closed with residual owned-path changes still uncommitted, treat the closeout as incomplete
• if the issue comment says work landed in the isolated branch but the commit actually landed on another checkout, post a correction/update before closeout

Recovery pattern when commit lands in the wrong checkout

Observed failure mode:

• Codex was launched from an isolated worktree
• Codex reported success and produced a valid commit
• the commit actually landed on local main instead of the intended issue worktree branch
• the intended worktree remained unchanged

Safe recovery:

1. identify the real landed commit hash
2. verify the diff and tests in the checkout where it actually landed
3. cherry-pick that exact commit into the intended clean worktree/branch
4. re-run the targeted validation in the intended worktree
5. treat the clean worktree commit as the authoritative execution result for push/closeout

This is distinct from the older “residual dirty files” failure mode: the code may be correct, but it is landed in the wrong branch context and must be re-homed before integration/closeout.

Decision rules

Case A — clean success

Criteria:

• all claimed files appear in the commit
• no owned-path files remain dirty
• issue comment matches actual commit Action:
• accept the run as complete

Case B — partial landing with residual owned-path edits

Criteria:

• some claimed files are not in the commit
• those files remain modified in the working tree
• issue may already be closed Action:
• do NOT assume full completion
• create a tiny follow-up commit for the missing owned-path files, OR reopen the issue if the gap is material
• document the discrepancy in the next GitHub comment

Case C — false success comment

Criteria:

• worker claimed success but commit does not contain the core deliverable Action:
• reopen or continue the issue immediately
• do not treat the run as landed

Recommended workflow

1. Capture Codex’s reported outputs:

• commit hash
• changed file list
• GitHub comment URL
• issue closed/open status

2. Run:

git show --stat --name-only <commit>
git status --short
gh issue view <issue> --json state,comments

3. Compare three surfaces:

• Codex summary
• actual commit contents
• residual working tree state

4. Only then decide whether the implementation is truly done.

Workspace-hub-specific lessons

In workspace-hub, this matters when:

• docs or generated files violate local repo conventions
• some wiki/domain files are already oversized or shaped in ways that trip repo expectations
• the run stages only a subset of the owned-path edits
• a Codex run launched from an isolated worktree may still create the commit on an unexpected local branch / checkout, even when the orchestrator passed the intended worktree as cwd

Concrete example pattern A:

• worker committed 10 files
• claimed 12 intended updates
• 2 wiki AGENTS.md files were still modified in working tree
• issue was already closed
• correct response was to treat the issue as substantially complete but with a small residual follow-up

Concrete example pattern B:

• orchestrator launched Codex -p from a clean issue worktree
• Codex reported success and a commit hash
• the intended issue worktree branch did not move
• the reported commit actually landed on the dirty local main checkout instead
• correct response was:
  1. verify the reported commit hash really contains the claimed file set
  2. confirm which branch/worktree actually contains that commit
  3. cherry-pick the validated commit into the clean execution worktree
  4. re-run the targeted tests in the clean worktree
  5. treat the clean worktree commit as the authoritative execution artifact for push/closeout

Add these checks when the worker was supposed to run in an isolated worktree:

• git branch --contains <commit> from the parent repo
• git log --oneline -3 in both the intended worktree and the default/main checkout
• verify the expected issue branch tip actually advanced

If the commit landed on the wrong local branch but the diff/tests are valid, prefer cherry-picking into the clean worktree over trying to salvage closeout directly from the dirty checkout. If the commit landed on the wrong local branch but the diff/tests are valid, prefer cherry-picking into the clean worktree over trying to salvage closeout directly from the dirty checkout.

Separate remote landing from parent-checkout state

Another live-use failure mode:

• Codex runs in a clean issue worktree
• the commit is pushed successfully to origin/main
• GitHub issues auto-close correctly
• but the user's current parent checkout (/mnt/local-analysis/workspace-hub) is still dirty and remains one commit behind remote main

This is easy to misreport as "everything is updated locally" when only the remote and worker branch are updated.

Required post-push checks when working from a side worktree:

1. verify the push target really contains the commit

git fetch origin
git rev-parse <commit>
git rev-parse origin/main
git branch --contains <commit>

2. separately inspect the parent/default checkout state

cd <parent-checkout>
git status --short
git rev-list --left-right --count HEAD...origin/main

3. report these as two different truths:

• remote landed state (did the change reach origin/main?)
• current local checkout state (is the user's working checkout updated/clean?)

Decision rule:

• if remote landed but parent checkout is dirty/behind, do not say the repo is fully synced locally
• say the implementation landed remotely and the parent checkout still needs an explicit sync/reconciliation step
• avoid auto-pulling into a dirty parent checkout unless the user asked for that reconciliation work

Output template for post-run review

Use this structure when reporting your verification:

• Commit landed: <hash>
• Issue state: open/closed
• Claimed changed files: N
• Actually committed files: N
• Residual owned-path files still dirty: list or none
• Verdict: complete / substantially complete with follow-up / incomplete
• Next action: none / tiny fixup commit / reopen and continue

Pitfalls

• Trusting the worker’s final summary without checking git show
• Looking only at git status and not the actual commit
• Missing residual issue-owned files because the repo has lots of unrelated dirt
• Treating an auto-closed issue as authoritative proof of completeness

Minimal command set

git show --stat --name-only <commit>
git status --short
gh issue view <issue> --json state,comments

Use this every time a Codex run claims success on a dirty repo.