[BUG] Worktree provisioning writes tracked hook config to shared info/exclude

[StirlingGoetz]

Description

Summary

With scm.isolation = "worktree" and the Codex adapter, worktree provisioning adds /.codex/hooks.json to the repository's shared .git/info/exclude, even when .codex/hooks.json is already tracked and was not modified during provisioning.

This makes the tracked hook configuration appear ignored and can break repository-hygiene or pre-commit checks.

Environment

• bmad-loop: 0.9.0
• Installed source revision: 232f3f7159004e960e786a6568ebe79daecf388d
• Upstream main also affected at: ad22f7966b0d0626bea3a22f0617f55c875b7810
• Adapter: Codex
• Git: 2.54.0
• OS: Linux
• SCM policy:
  • isolation = "worktree"
  • branch_per = "story"
  • seed_adapter_defaults = true

Steps to reproduce

Steps to reproduce

1. Create a Git repository with a tracked .codex/hooks.json:

   git add .codex/hooks.json
   git commit -m "Track Codex hook configuration"Confirm no tracked files are ignored:

git ls-files -ci --exclude-standard

Configure bmad-loop to use the Codex adapter and worktree isolation.

Start a run that provisions an isolated story worktree.

Inspect the common Git exclude file:
git check-ignore --no-index -v .codex/hooks.json

Check for tracked-and-ignored files again:
git ls-files -ci --exclude-standard

Expected behavior

Expected behavior
Worktree provisioning should:
Never make an already-tracked file ignored.
Avoid changing ignore behavior for the main checkout or unrelated worktrees.
Exclude only untracked files actually created by provisioning.
Remove any provisioning-owned metadata during worktree/run cleanup.

Actual behavior

Actual behavior
After provisioning:
.git/info/exclude:...:/.codex/hooks.json .codex/hooks.json
and:
.codex/hooks.json
is returned by git ls-files -ci --exclude-standard.
provision_worktree() unconditionally adds every non-hookless profile's hook configuration to the exclusion set:
patterns |= {
f"/{p.hooks.config_path}"
for p in profiles
if not p.hookless
}
_worktree_local_exclude() then resolves git rev-parse --git-common-dir and writes to:
common_dir / "info" / "exclude"
For a linked worktree, that is the main repository's shared Git directory. The exclusion therefore affects the main checkout and every linked worktree; it is not worktree-local.
Deleting the run or its worktree does not remove the shared exclusion entry.

Impact
Repositories that reject tracked-and-ignored files can pass preflight and then begin failing immediately after bmad-loop provisions its story worktree.
In our run, this blocked the repository commit/review gate and resulted in a CRITICAL review escalation. The implementation remained isolated and was never merged, but the shared .git/info/exclude residue required manual cleanup.
Suggested fix
Before adding a path to the exclusion set, check whether it is tracked:
git ls-files --error-unmatch --
Never exclude tracked paths.

Track which hook or skill paths were actually created or modified during provisioning; do not add every configured path unconditionally.

Do not describe or implement /info/exclude as worktree-local. Use genuinely worktree-scoped state where possible, or explicitly manage shared entries with ownership and cleanup.

Add a regression test that:
Starts with a tracked .codex/hooks.json.
Provisions a linked worktree.
Asserts git ls-files -ci --exclude-standard remains empty in both the main checkout and linked worktree.
Deletes the run/worktree and verifies no exclude residue remains.

Temporary workaround
After worktree provisioning, remove /.codex/hooks.json from the common repository's .git/info/exclude.
Removing it before the run is insufficient because provisioning adds it again.

The upstream issue tracker currently reports

Screenshots

No response

Which area is this for?

Orchestrator / control loop

bmad-loop Version

0.9.0

Which coding CLI are you using?

Codex (codex)

Operating System

Linux

Relevant log output

codex-cli 0.144.6

Diagnostic dump (bmad-loop diagnose)

PAUSED: CRITICAL escalation from review session: ### Status

• Final status: blocked.
• Blocking condition: the required scoped checkpoint cannot commit because bun run check:repo-hygiene rejects the pre-existing tracked-and-ignored .codex/hooks.json; bypassing the repository hook or changing that out-of-scope file was not authorized.
• Secret scan: PASS for the five scoped review files.

Confirm

• I've searched for existing issues
• If I attached a diagnose dump, I reviewed it and confirmed it contains no PII, secrets, or project-specific information
• I'm using the latest version

[coderabbitai]

⚠️ Possible Duplicate Issue(s)

• provision_worktree's exclude patterns are repo-wide and permanent: new files under .claude/skills silently stop being staged in the main checkout #384

🔗 Related PRs

#182 - fix(worktree): degrade post-merge teardown failures instead of crashing the run (#139) [merged]
#257 - feat(worktree): seed the absent children of an existing seed dir (#235) [merged]
#373 - fix(install): guard the worktree exclude's filesystem tail (#359) [merged]
#376 - fix(install): close the exclude helper's two residual holes (#374, #375) [merged]
#385 - fix(install): scope the worktree git-add shield per-worktree (#384) [open]

---

📝 Issue Planner

_{Check the box below or use the @coderabbitai plan command to generate an implementation plan and prompts that you can use with your favorite coding assistant.}

• Create Plan

---

🧪 Issue enrichment is currently in open beta.

You can configure auto-planning by selecting labels in the issue_enrichment configuration.

To disable automatic issue enrichment, add the following to your .coderabbit.yaml:

issue_enrichment:
  auto_enrich:
    enabled: false

💬 Have feedback or questions? Drop into our discord!