Handle squash-merged PR branches in automated cleanup

.githooks/post-merge

@@ -37,6 +37,7 @@ fi
 "$node_bin" "$cli_path" cleanup \
   --target "$repo_root" \
   --base "$base_branch" \
+  --include-pr-merged \
   --keep-clean-worktrees >/dev/null 2>&1 || true
 
 exit 0

bin/multiagent-safety.js

@@ -2404,6 +2404,7 @@ function parseCleanupArgs(rawArgs) {
     forceDirty: false,
     keepRemote: false,
     keepCleanWorktrees: false,
+    includePrMerged: false,
     idleMinutes: 0,
     watch: false,
     intervalSeconds: 60,
@@ -2455,6 +2456,10 @@ function parseCleanupArgs(rawArgs) {
       options.keepCleanWorktrees = true;
       continue;
     }
+    if (arg === '--include-pr-merged') {
+      options.includePrMerged = true;
+      continue;
+    }
     if (arg === '--idle-minutes') {
       const next = rawArgs[index + 1];
       if (!next) {
@@ -4564,6 +4569,9 @@ function cleanup(rawArgs) {
   if (!options.keepCleanWorktrees) {
     args.push('--only-dirty-worktrees');
   }
+  if (options.includePrMerged) {
+    args.push('--include-pr-merged');
+  }
   if (options.idleMinutes > 0) {
     args.push('--idle-minutes', String(options.idleMinutes));
   }

scripts/agent-worktree-prune.sh

@@ -8,11 +8,16 @@ FORCE_DIRTY=0
 DELETE_BRANCHES=0
 DELETE_REMOTE_BRANCHES=0
 ONLY_DIRTY_WORKTREES=0
+INCLUDE_PR_MERGED=0
 TARGET_BRANCH=""
 IDLE_MINUTES=0
 NOW_EPOCH_RAW="${MUSAFETY_PRUNE_NOW_EPOCH:-}"
 IDLE_SECONDS=0
 NOW_EPOCH=0
+GH_BIN="${MUSAFETY_GH_BIN:-gh}"
+PR_MERGED_LOOKUP_DISABLED=0
+PR_MERGED_LOOKUP_LOADED=0
+declare -A MERGED_PR_BRANCHES=()
 
 if [[ -n "$BASE_BRANCH" ]]; then
   BASE_BRANCH_EXPLICIT=1
@@ -45,6 +50,10 @@ while [[ $# -gt 0 ]]; do
       ONLY_DIRTY_WORKTREES=1
       shift
       ;;
+    --include-pr-merged)
+      INCLUDE_PR_MERGED=1
+      shift
+      ;;
     --branch)
       TARGET_BRANCH="${2:-}"
       shift 2
@@ -55,7 +64,7 @@ while [[ $# -gt 0 ]]; do
       ;;
     *)
       echo "[agent-worktree-prune] Unknown argument: $1" >&2
-      echo "Usage: $0 [--base <branch>] [--dry-run] [--force-dirty] [--delete-branches] [--delete-remote-branches] [--only-dirty-worktrees] [--branch <agent/...>] [--idle-minutes <minutes>]" >&2
+      echo "Usage: $0 [--base <branch>] [--dry-run] [--force-dirty] [--delete-branches] [--delete-remote-branches] [--only-dirty-worktrees] [--include-pr-merged] [--branch <agent/...>] [--idle-minutes <minutes>]" >&2
       exit 1
       ;;
   esac
@@ -101,6 +110,44 @@ resolve_base_branch() {
   printf '%s' ""
 }
 
+load_merged_pr_branches() {
+  if [[ "$INCLUDE_PR_MERGED" -ne 1 ]]; then
+    return 1
+  fi
+  if [[ "$PR_MERGED_LOOKUP_DISABLED" -eq 1 ]]; then
+    return 1
+  fi
+  if [[ "$PR_MERGED_LOOKUP_LOADED" -eq 1 ]]; then
+    return 0
+  fi
+  if ! command -v "$GH_BIN" >/dev/null 2>&1; then
+    PR_MERGED_LOOKUP_DISABLED=1
+    return 1
+  fi
+
+  local merged_branches=""
+  merged_branches="$(
+    "$GH_BIN" pr list --state merged --base "$BASE_BRANCH" --limit 200 --json headRefName --jq '.[].headRefName' 2>/dev/null || true
+  )"
+  if [[ -n "$merged_branches" ]]; then
+    while IFS= read -r merged_branch; do
+      [[ -z "$merged_branch" ]] && continue
+      MERGED_PR_BRANCHES["$merged_branch"]=1
+    done <<< "$merged_branches"
+  fi
+  PR_MERGED_LOOKUP_LOADED=1
+  return 0
+}
+
+branch_has_merged_pr() {
+  local branch="$1"
+  if [[ "$INCLUDE_PR_MERGED" -ne 1 ]]; then
+    return 1
+  fi
+  load_merged_pr_branches || return 1
+  [[ -n "${MERGED_PR_BRANCHES[$branch]:-}" ]]
+}
+
 if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 && -z "$BASE_BRANCH" ]]; then
   echo "[agent-worktree-prune] --base requires a non-empty branch name." >&2
   exit 1
@@ -342,6 +389,7 @@ process_entry() {
   fi
 
   local remove_reason=""
+  local branch_delete_mode="safe"
 
   if [[ -z "$branch_ref" ]]; then
     remove_reason="detached-worktree"
@@ -352,6 +400,9 @@ process_entry() {
       if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
         remove_reason="merged-agent-branch"
       fi
+    elif [[ "$DELETE_BRANCHES" -eq 1 ]] && branch_has_merged_pr "$branch"; then
+      remove_reason="merged-agent-pr"
+      branch_delete_mode="force"
     elif [[ "$ONLY_DIRTY_WORKTREES" -eq 1 ]] && is_clean_worktree "$wt"; then
       remove_reason="clean-agent-worktree"
     fi
@@ -383,13 +434,19 @@ process_entry() {
 
   if git -C "$repo_root" show-ref --verify --quiet "refs/heads/${branch}" && ! branch_has_worktree "$branch"; then
     if [[ "$branch" == agent/* && "$DELETE_BRANCHES" -eq 1 ]]; then
-      if run_cmd git -C "$repo_root" branch -d "$branch" >/dev/null 2>&1; then
+      local delete_flag="-d"
+      local deleted_label="merged"
+      if [[ "$branch_delete_mode" == "force" ]]; then
+        delete_flag="-D"
+        deleted_label="merged PR"
+      fi
+      if run_cmd git -C "$repo_root" branch "$delete_flag" "$branch" >/dev/null 2>&1; then
         removed_branches=$((removed_branches + 1))
-        echo "[agent-worktree-prune] Deleted merged branch: ${branch}"
+        echo "[agent-worktree-prune] Deleted ${deleted_label} branch: ${branch}"
         if [[ "$DELETE_REMOTE_BRANCHES" -eq 1 ]]; then
           if git -C "$repo_root" ls-remote --exit-code --heads origin "$branch" >/dev/null 2>&1; then
             run_cmd git -C "$repo_root" push origin --delete "$branch" >/dev/null 2>&1 || true
-            echo "[agent-worktree-prune] Deleted merged remote branch: ${branch}"
+            echo "[agent-worktree-prune] Deleted ${deleted_label} remote branch: ${branch}"
           fi
         fi
       fi
@@ -436,14 +493,27 @@ if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
     if ! branch_idle_gate "$branch" "" "stale-merged-branch"; then
       continue
     fi
+    local merged_by_ancestor=0
+    local merged_by_pr=0
     if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
-      if run_cmd git -C "$repo_root" branch -d "$branch" >/dev/null 2>&1; then
+      merged_by_ancestor=1
+    elif branch_has_merged_pr "$branch"; then
+      merged_by_pr=1
+    fi
+    if [[ "$merged_by_ancestor" -eq 1 || "$merged_by_pr" -eq 1 ]]; then
+      local delete_flag="-d"
+      local deleted_label="merged"
+      if [[ "$merged_by_pr" -eq 1 && "$merged_by_ancestor" -eq 0 ]]; then
+        delete_flag="-D"
+        deleted_label="merged PR"
+      fi
+      if run_cmd git -C "$repo_root" branch "$delete_flag" "$branch" >/dev/null 2>&1; then
         removed_branches=$((removed_branches + 1))
-        echo "[agent-worktree-prune] Deleted stale merged branch: ${branch}"
+        echo "[agent-worktree-prune] Deleted stale ${deleted_label} branch: ${branch}"
         if [[ "$DELETE_REMOTE_BRANCHES" -eq 1 ]]; then
           if git -C "$repo_root" ls-remote --exit-code --heads origin "$branch" >/dev/null 2>&1; then
             run_cmd git -C "$repo_root" push origin --delete "$branch" >/dev/null 2>&1 || true
-            echo "[agent-worktree-prune] Deleted stale merged remote branch: ${branch}"
+            echo "[agent-worktree-prune] Deleted stale ${deleted_label} remote branch: ${branch}"
           fi
         fi
       fi

templates/githooks/post-merge

@@ -37,6 +37,7 @@ fi
 "$node_bin" "$cli_path" cleanup \
   --target "$repo_root" \
   --base "$base_branch" \
+  --include-pr-merged \
   --keep-clean-worktrees >/dev/null 2>&1 || true
 
 exit 0

test/install.test.js

@@ -1857,6 +1857,7 @@ test('post-merge auto-runs cleanup on base branch and skips non-base branches',
   assert.match(invocations[0], /^cleanup /);
   assert.match(invocations[0], new RegExp(`--target ${escapeRegexLiteral(repoDir)}`));
   assert.match(invocations[0], /--base dev/);
+  assert.match(invocations[0], /--include-pr-merged/);
   assert.match(invocations[0], /--keep-clean-worktrees/);
 
   result = runCmd('git', ['checkout', '-b', 'feature/post-merge-skip'], repoDir);
@@ -3333,6 +3334,52 @@ test('cleanup command keeps unmerged agent branch refs but removes clean agent w
   assert.equal(localBranch.status, 0, 'cleanup should keep unmerged local branch');
 });
 
+test('cleanup command can remove squash-merged agent branches via merged PR detection', () => {
+  const repoDir = initRepo();
+  seedCommit(repoDir);
+
+  let result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const worktreePath = path.join(repoDir, '.omx', 'agent-worktrees', 'agent__cleanup-pr-merged');
+  result = runCmd('git', ['worktree', 'add', '-b', 'agent/test-cleanup-pr-merged', worktreePath, 'dev'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  fs.writeFileSync(path.join(worktreePath, 'feature.txt'), 'feature branch commit\n', 'utf8');
+  result = runCmd('git', ['-C', worktreePath, 'add', 'feature.txt'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['-C', worktreePath, 'commit', '-m', 'feature commit'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const { fakePath: fakeGhPath } = createFakeGhScript(
+    'if [[ "$1" == "pr" && "$2" == "list" ]]; then\n' +
+      '  printf \'%s\\n\' "agent/test-cleanup-pr-merged"\n' +
+      '  exit 0\n' +
+      'fi\n' +
+      'exit 1',
+  );
+
+  result = runNodeWithEnv(
+    [
+      'cleanup',
+      '--target',
+      repoDir,
+      '--branch',
+      'agent/test-cleanup-pr-merged',
+      '--keep-remote',
+      '--keep-clean-worktrees',
+      '--include-pr-merged',
+    ],
+    repoDir,
+    { MUSAFETY_GH_BIN: fakeGhPath },
+  );
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const localBranch = runCmd('git', ['show-ref', '--verify', '--quiet', 'refs/heads/agent/test-cleanup-pr-merged'], repoDir);
+  assert.notEqual(localBranch.status, 0, 'cleanup should remove merged PR local branch');
+  assert.equal(fs.existsSync(worktreePath), false, 'cleanup should remove merged PR worktree');
+});
+
 test('cleanup command watch mode defaults to 10-minute idle threshold and supports one-cycle execution', () => {
   const repoDir = initRepo();
   const scriptsDir = path.join(repoDir, 'scripts');