Merge pull request 'feat: add worktree cleanup audit integrity (Closes #404)' (#417) from feat/issue-404-worktree-cleanup-audit into master

skills/llm-project-workflow/templates/worktree-cleanup.md

@@ -26,3 +26,43 @@ Steps:
 
 Handoff: merge confirmed, issue closed, branch+worktree removed, checkout clean.
 ```
+
+## Branches cleanup audit integrity (#404)
+
+Any bulk or multi-path cleanup under `branches/` must capture auditable before/after
+identity for every initial directory and registered worktree. Use
+`worktree_cleanup_audit.capture_cleanup_snapshot` before and after cleanup, record
+every intentional removal in a removal log (path, method, order, timestamp,
+pre-removal proof), then run `reconcile_cleanup_audit` and
+`assess_cleanup_audit_integrity`.
+
+The cleanup report must include a reconciliation table:
+
+* initial count
+* removed count
+* preserved count
+* missing-unexplained count
+* final count
+
+Fail closed when:
+
+* a preserved (active PR, dirty, claim/lease, or unsafe) worktree disappears without
+  a removal log entry or explicit explanation
+* the removal log omits a removed clean-stale path
+* final counts do not reconcile with initial minus removed
+
+If another session removes or mutates a worktree during cleanup, record the path
+under explained missing entries — never treat silent disappearance as success.
+
+## Bulk `branches/` cleanup audit (#404)
+
+Before removing multiple session-owned worktrees:
+
+1. Call `gitea_capture_branches_worktree_snapshot` and record the before snapshot.
+2. Remove only paths classified as `clean_stale_removable` with explicit per-path proof.
+3. Log every removal with path, method, and timestamp/order.
+4. Capture an after snapshot with the same tool.
+5. Call `gitea_assess_worktree_cleanup_integrity` with before, after, and the removal log.
+6. Fail closed when any protected path (active PR, dirty, claim/lease) disappears
+   without an explained state transition.
+7. Final report must include the reconciliation table and `git worktree list` proof.