@imdeadpool/guardex 7.0.24 → 7.0.25

package/README.md

@@ -140,7 +140,7 @@ That's it. Install and update via `@imdeadpool/guardex`. Setup installs the mini
 </div>
 
 > [!NOTE]
-> In this repo, `CLAUDE.md` is a symlink to `AGENTS.md`, so Claude reads the same contract. Optional Codex/Claude companion files are installed at the user level with `gx install-agent-skills`, not copied into each repo.
+> In this repo, `CLAUDE.md` is a symlink to `AGENTS.md`, so Claude reads the same contract. Optional Codex/Claude companion files still install at the user level with `gx install-agent-skills`, while the generic repo skill catalog is available through `npx skills add recodeee/` or directly via `npx skills add recodeee/gitguardex`.
 
 ### Decision flow
 
@@ -266,7 +266,7 @@ To install the real companion into local VS Code from a GitGuardex-wired repo:
 node scripts/install-vscode-active-agents-extension.js
 ```
 
-It adds an `Active Agents` view to the Source Control container, groups each live repo into `ACTIVE AGENTS` and `CHANGES` sections, splits `ACTIVE AGENTS` into `BLOCKED`, `WORKING NOW`, `IDLE`, `STALLED`, and `DEAD` when those states are present, mirrors the selected session or active-agent count in the VS Code status bar, reads `.omx/state/active-sessions/*.json`, derives session state from git conflict markers, dirty worktree status, PID liveness, and recent file mtimes, and surfaces working/dead counts in the repo/header affordances. Reload the VS Code window after install.
+It adds a dedicated `Active Agents` Activity Bar container with a hive icon, shows the live active-agent count as a badge on that icon, groups each live repo into `ACTIVE AGENTS` and `CHANGES` sections, splits `ACTIVE AGENTS` into `BLOCKED`, `WORKING NOW`, `IDLE`, `STALLED`, and `DEAD` when those states are present, mirrors the selected session or active-agent count in the VS Code status bar, reads `.omx/state/active-sessions/*.json`, derives session state from git conflict markers, dirty worktree status, PID liveness, and recent file mtimes, and surfaces working/dead counts in the repo/header affordances. Reload the VS Code window after install.
 
 ---
 
@@ -459,6 +459,23 @@ npm i -g oh-my-claude-sisyphus@latest
 Repo: <https://github.com/Yeachan-Heo/oh-my-claudecode>
 [![GitHub stars](https://img.shields.io/github/stars/Yeachan-Heo/oh-my-claudecode?style=social)](https://github.com/Yeachan-Heo/oh-my-claudecode)
 
+### GitGuardex skills - install the repo skill catalog through `npx skills`
+
+For agents that already support the generic `skills` installer flow, GitGuardex now exposes its repo skill catalog directly. You can start from the broader `recodeee` source or jump straight into this repo's catalog.
+
+```sh
+npx skills add recodeee/
+```
+
+```sh
+npx skills add recodeee/gitguardex
+```
+
+This repo currently exposes `gitguardex` and `guardex-merge-skills-to-dev` through that flow. If the picker does not show a separate `guardex` skill, that is expected: `guardex` remains the legacy CLI alias, while the repo skill itself is named `gitguardex`. Use `gx install-agent-skills` when you want the Codex/Claude user-home startup files instead of the generic `skills` catalog.
+
+Repo: <https://github.com/recodeee/gitguardex>
+[![GitHub stars](https://img.shields.io/github/stars/recodeee/gitguardex?style=social)](https://github.com/recodeee/gitguardex)
+
 ### Caveman — output compression for long agent runs
 
 Ultra-compressed response mode for Claude/Codex-style agents. Useful when you want less output-token churn during long reviews, debug loops, or multi-agent sessions.
@@ -609,7 +626,7 @@ vscode/guardex-active-agents/README.md
 
 Legacy compatibility note: older repos may still contain repo-local workflow scripts under `scripts/`. Direct `gx branch ...`, `gx locks ...`, `gx finish`, `gx cleanup`, `gx merge`, and `gx migrate` do not require them. `gx migrate` removes those leftover workflow shims by default. The CLI still honors repo-local `scripts/review-bot-watch.sh` and `scripts/codex-agent.sh` when they are already present so older repos can keep working during migration.
 
-Optional Codex/Claude user-level companions still install with `gx install-agent-skills`; they are not copied into each repo.
+Optional Codex/Claude user-level companions still install with `gx install-agent-skills`; the generic repo skill catalog is available with `npx skills add recodeee/` or directly via `npx skills add recodeee/gitguardex`. Neither path copies those user-home files into each repo.
 
 ---
 
@@ -672,6 +689,11 @@ npm pack --dry-run
 <details>
 <summary><strong>v7.x</strong></summary>
 
+### v7.0.25
+- Bumped `@imdeadpool/guardex` from `7.0.24` to `7.0.25` so npm and GitHub Releases can ship the current `main` payload.
+- The bundled `GitGuardex Active Agents` VS Code companion now self-heals stale repo-scan ignore settings in older repos, keeps plain managed sandboxes visible in Source Control, and preserves cleanup truth so the tree matches actual sandbox state.
+- Bumped the shipped Active Agents companion manifests from `0.0.8` to `0.0.9` so local VS Code installs can pick up the newer workspace build and show the refreshed extension version from this release.
+
 ### v7.0.24
 - Bumped `@imdeadpool/guardex` from `7.0.23` to `7.0.24` so GitHub Releases and the npm publish retry can advance together after `v7.0.23` landed on GitHub but not on npm.
 - Release verification no longer loses its base ref on tag-triggered runs, so the publish workflow keeps the history it needs before packing and publish checks.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@imdeadpool/guardex",
-  "version": "7.0.24",
+  "version": "7.0.25",
   "description": "Guardian T-Rex for your multi-agent repo. Isolated worktrees, file locks, and PR-only merges stop parallel Codex & Claude agents from overwriting each other's work. Auto-wires Oh My Codex, Oh My Claude, OpenSpec, and Caveman.",
   "license": "MIT",
   "preferGlobal": true,

package/src/cli/args.js

@@ -770,6 +770,7 @@ function parseFinishArgs(rawArgs, defaults = {}) {
     cleanup: defaults.cleanup ?? true,
     keepRemote: false,
     noAutoCommit: false,
+    parentGitlinkCommit: defaults.parentGitlinkCommit ?? true,
     failFast: false,
     commitMessage: '',
     mergeMode: defaults.mergeMode || 'pr',
@@ -865,6 +866,14 @@ function parseFinishArgs(rawArgs, defaults = {}) {
       options.noAutoCommit = true;
       continue;
     }
+    if (arg === '--parent-gitlink-commit') {
+      options.parentGitlinkCommit = true;
+      continue;
+    }
+    if (arg === '--no-parent-gitlink-commit') {
+      options.parentGitlinkCommit = false;
+      continue;
+    }
     if (arg === '--fail-fast') {
       options.failFast = true;
       continue;

package/src/context.js

@@ -129,6 +129,14 @@ const TEMPLATE_FILES = [
   'vscode/guardex-active-agents/session-schema.js',
   'vscode/guardex-active-agents/README.md',
   'vscode/guardex-active-agents/icon.png',
+  'vscode/guardex-active-agents/fileicons/gitguardex-fileicons.json',
+  'vscode/guardex-active-agents/fileicons/icons/agent.svg',
+  'vscode/guardex-active-agents/fileicons/icons/branch.svg',
+  'vscode/guardex-active-agents/fileicons/icons/config.svg',
+  'vscode/guardex-active-agents/fileicons/icons/hook.svg',
+  'vscode/guardex-active-agents/fileicons/icons/openspec.svg',
+  'vscode/guardex-active-agents/fileicons/icons/plan.svg',
+  'vscode/guardex-active-agents/fileicons/icons/spec.svg',
 ];
 
 const PACKAGE_ROOT_SOURCE_OVERRIDES = new Set([
@@ -139,6 +147,14 @@ const PACKAGE_ROOT_SOURCE_OVERRIDES = new Set([
   'vscode/guardex-active-agents/session-schema.js',
   'vscode/guardex-active-agents/README.md',
   'vscode/guardex-active-agents/icon.png',
+  'vscode/guardex-active-agents/fileicons/gitguardex-fileicons.json',
+  'vscode/guardex-active-agents/fileicons/icons/agent.svg',
+  'vscode/guardex-active-agents/fileicons/icons/branch.svg',
+  'vscode/guardex-active-agents/fileicons/icons/config.svg',
+  'vscode/guardex-active-agents/fileicons/icons/hook.svg',
+  'vscode/guardex-active-agents/fileicons/icons/openspec.svg',
+  'vscode/guardex-active-agents/fileicons/icons/plan.svg',
+  'vscode/guardex-active-agents/fileicons/icons/spec.svg',
 ]);
 
 const LEGACY_WORKFLOW_SHIM_SPECS = [
@@ -263,8 +279,12 @@ const AGENT_WORKTREE_RELATIVE_DIRS = [
 const MANAGED_REPO_SCAN_IGNORED_FOLDERS = [
   '.omx/agent-worktrees',
   '**/.omx/agent-worktrees',
+  '.omx/.tmp-worktrees',
+  '**/.omx/.tmp-worktrees',
   '.omc/agent-worktrees',
   '**/.omc/agent-worktrees',
+  '.omc/.tmp-worktrees',
+  '**/.omc/.tmp-worktrees',
 ];
 const MANAGED_GITIGNORE_PATHS = [
   '.omx/',
@@ -427,6 +447,8 @@ const AI_SETUP_PARTS = [
       'gx branch start "<task>" "<agent>"',
       'then gx locks claim --branch "<agent-branch>" <file...> -> inspect once -> patch once -> verify once -> gx branch finish',
       'batch discovery, git/PR, and CI by phase; avoid repeated peeks or stdin loops',
+      'checkpoint after each milestone: Task -> Done -> Current status -> Next; keep only the latest checkpoint(s) in active context',
+      'summarize tool results, keep stdin/process chatter ephemeral, and keep execution log separate from reasoning context',
     ],
     execLines: [
       'gx branch start "<task>" "<agent>"',

package/src/doctor/index.js

@@ -314,6 +314,118 @@ function doctorFinishFlowIsPending(output) {
   );
 }
 
+function verifyDoctorSandboxCleanup(repoRoot, metadata) {
+  const branchExists = Boolean(metadata.branch) && gitRefExists(repoRoot, `refs/heads/${metadata.branch}`);
+  const worktreeExists = Boolean(metadata.worktreePath) && fs.existsSync(metadata.worktreePath);
+
+  if (!branchExists && !worktreeExists) {
+    return {
+      status: 'verified',
+      note: 'doctor sandbox cleanup verified',
+    };
+  }
+
+  const cleanup = cleanupProtectedBaseSandbox(repoRoot, metadata);
+  const branchStillExists = Boolean(metadata.branch) && gitRefExists(repoRoot, `refs/heads/${metadata.branch}`);
+  const worktreeStillExists = Boolean(metadata.worktreePath) && fs.existsSync(metadata.worktreePath);
+  if (branchStillExists || worktreeStillExists) {
+    return {
+      status: 'failed',
+      note:
+        'doctor sandbox cleanup incomplete ' +
+        `(branch=${branchStillExists ? 'present' : 'missing'}, worktree=${worktreeStillExists ? 'present' : 'missing'})`,
+      cleanup,
+    };
+  }
+
+  return {
+    status: 'verified',
+    note: 'doctor sandbox cleanup verified',
+    cleanup,
+  };
+}
+
+function verifyDoctorSandboxRemoteCleanup(repoRoot, metadata) {
+  if (!metadata.branch || !hasOriginRemote(repoRoot)) {
+    return {
+      status: 'skipped',
+      note: 'doctor sandbox remote cleanup skipped',
+    };
+  }
+
+  const remoteBefore = run(
+    'git',
+    ['-C', repoRoot, 'ls-remote', '--heads', 'origin', metadata.branch],
+    { timeout: 20_000 },
+  );
+  if (isSpawnFailure(remoteBefore)) {
+    throw remoteBefore.error;
+  }
+  if (remoteBefore.status !== 0) {
+    return {
+      status: 'failed',
+      note: 'doctor sandbox remote branch inspection failed',
+      stdout: remoteBefore.stdout || '',
+      stderr: remoteBefore.stderr || '',
+    };
+  }
+  if (!String(remoteBefore.stdout || '').trim()) {
+    return {
+      status: 'verified',
+      note: 'doctor sandbox remote cleanup verified',
+    };
+  }
+
+  const deleteResult = run(
+    'git',
+    ['-C', repoRoot, 'push', 'origin', '--delete', metadata.branch],
+    { timeout: 30_000 },
+  );
+  if (isSpawnFailure(deleteResult)) {
+    throw deleteResult.error;
+  }
+  if (deleteResult.status !== 0) {
+    return {
+      status: 'failed',
+      note: 'doctor sandbox remote branch cleanup failed',
+      stdout: deleteResult.stdout || '',
+      stderr: deleteResult.stderr || '',
+    };
+  }
+
+  const remoteAfter = run(
+    'git',
+    ['-C', repoRoot, 'ls-remote', '--heads', 'origin', metadata.branch],
+    { timeout: 20_000 },
+  );
+  if (isSpawnFailure(remoteAfter)) {
+    throw remoteAfter.error;
+  }
+  if (remoteAfter.status !== 0) {
+    return {
+      status: 'failed',
+      note: 'doctor sandbox remote cleanup recheck failed',
+      stdout: remoteAfter.stdout || '',
+      stderr: remoteAfter.stderr || '',
+    };
+  }
+  if (String(remoteAfter.stdout || '').trim()) {
+    return {
+      status: 'failed',
+      note: 'doctor sandbox remote branch still present after cleanup',
+      stdout: remoteAfter.stdout || '',
+      stderr: remoteAfter.stderr || '',
+    };
+  }
+
+  return {
+    status: 'verified',
+    note: 'doctor sandbox remote cleanup verified',
+    stdout: deleteResult.stdout || '',
+    stderr: deleteResult.stderr || '',
+  };
+}
+
 function finishDoctorSandboxBranch(blocked, metadata, options = {}) {
   if (!hasOriginRemote(blocked.repoRoot)) {
     return {
@@ -353,8 +465,8 @@ function finishDoctorSandboxBranch(blocked, metadata, options = {}) {
 
   const finishResult = runPackageAsset(
     'branchFinish',
-    ['--branch', metadata.branch, '--base', blocked.branch, '--via-pr', waitForMergeArg, '--cleanup'],
-    { cwd: metadata.worktreePath, timeout: finishTimeoutMs },
+    ['--branch', metadata.branch, '--base', blocked.branch, '--via-pr', waitForMergeArg, '--no-cleanup'],
+    { cwd: blocked.repoRoot, timeout: finishTimeoutMs },
   );
   if (isSpawnFailure(finishResult)) {
     return {
@@ -384,11 +496,52 @@ function finishDoctorSandboxBranch(blocked, metadata, options = {}) {
     };
   }
 
+  let cleanupVerification;
+  try {
+    cleanupVerification = verifyDoctorSandboxCleanup(blocked.repoRoot, metadata);
+  } catch (error) {
+    return {
+      status: 'failed',
+      note: `doctor sandbox cleanup verification failed: ${error.message}`,
+      stdout: finishResult.stdout || '',
+      stderr: finishResult.stderr || '',
+    };
+  }
+  if (cleanupVerification.status === 'failed') {
+    return {
+      status: 'failed',
+      note: cleanupVerification.note,
+      stdout: finishResult.stdout || '',
+      stderr: finishResult.stderr || '',
+    };
+  }
+
+  let remoteCleanupVerification;
+  try {
+    remoteCleanupVerification = verifyDoctorSandboxRemoteCleanup(blocked.repoRoot, metadata);
+  } catch (error) {
+    return {
+      status: 'failed',
+      note: `doctor sandbox remote cleanup verification failed: ${error.message}`,
+      stdout: finishResult.stdout || '',
+      stderr: finishResult.stderr || '',
+    };
+  }
+  if (remoteCleanupVerification.status === 'failed') {
+    return {
+      status: 'failed',
+      note: remoteCleanupVerification.note,
+      stdout: [finishResult.stdout || '', remoteCleanupVerification.stdout || ''].filter(Boolean).join('\n'),
+      stderr: [finishResult.stderr || '', remoteCleanupVerification.stderr || ''].filter(Boolean).join('\n'),
+    };
+  }
+
   return {
     status: 'completed',
-    note: 'doctor sandbox finish flow completed',
-    stdout: finishResult.stdout || '',
-    stderr: finishResult.stderr || '',
+    note: 'doctor sandbox finish flow completed and cleanup verified',
+    stdout: [finishResult.stdout || '', remoteCleanupVerification.stdout || ''].filter(Boolean).join('\n'),
+    stderr: [finishResult.stderr || '', remoteCleanupVerification.stderr || ''].filter(Boolean).join('\n'),
+    cleanup: cleanupVerification.cleanup,
   };
 }
 

package/src/finish/index.js

@@ -317,6 +317,7 @@ function finish(rawArgs, defaults = {}) {
       if (options.keepRemote) {
         finishArgs.push('--keep-remote-branch');
       }
+      finishArgs.push(options.parentGitlinkCommit ? '--parent-gitlink-commit' : '--no-parent-gitlink-commit');
 
       if (options.dryRun) {
         console.log(`[${TOOL_NAME}] [dry-run] Would run: gx branch finish ${finishArgs.join(' ')}`);

package/templates/AGENTS.multiagent-safety.md

@@ -21,8 +21,11 @@ Default: less word, same proof.
 - Front-load scaffold/path discovery into one grouped inspection pass. Avoid serial `ls` / `find` / `rg` / `cat` retries that only rediscover the same path state.
 - Treat repeated `write_stdin`, repeated `sed` / `cat` peeks, and tiny diagnostic follow-up checks as strong negative signals. If they appear alongside climbing input cost, stop the probe loop and batch the next phase.
 - Tool / hook summaries stay tiny: command, status, last meaningful lines only. Drop routine hook boilerplate.
+- Keep raw terminal interaction out of long-lived context. For `write_stdin` or interactive babysitting, retain only process, action sent, current result, and next action.
+- Keep execution log separate from reasoning context: full commands/stdout belong in logs, while prompt context keeps only the latest 1-2 checkpoints plus the newest tool-result summary.
 - Treat local edit/commit, remote publish/PR, CI diagnosis, and cleanup as bounded phases. Do not spend fresh narration or approval turns on obvious safe follow-ons inside an already authorized phase unless the risk changes.
 - When a session turns fragmented, collapse back to inspect once, patch once, verify once, and summarize once.
+- Use a fixed checkpoint shape when compacting: `Task`, `Done`, `Current status`, and `Next`.
 - Keep `.omx/notepad.md` lean: live handoffs only. Use exactly `branch`, `task`, `blocker`, `next step`, and `evidence`; move narrative proof into OpenSpec artifacts, PRs, or command output.
 
 ## OMX Caveman Style

package/templates/codex/skills/guardex-merge-skills-to-dev/SKILL.md

@@ -9,6 +9,7 @@ Use this skill when you only want to promote Codex skill file updates into the b
 
 ## What this merges
 
+- `skills/**/SKILL.md`
 - `.codex/skills/**/SKILL.md`
 - `templates/codex/skills/**/SKILL.md`
 
@@ -33,7 +34,7 @@ gx branch start "merge-skill-files-to-${BASE_BRANCH}" "skill-merge" "$BASE_BRANC
 
 ```sh
 SOURCE_BRANCH="<agent-branch>"
-git checkout "$SOURCE_BRANCH" -- ':(glob).codex/skills/**/SKILL.md' ':(glob)templates/codex/skills/**/SKILL.md'
+git checkout "$SOURCE_BRANCH" -- ':(glob)skills/**/SKILL.md' ':(glob).codex/skills/**/SKILL.md' ':(glob)templates/codex/skills/**/SKILL.md'
 ```
 
 5. Verify scope before commit:
@@ -46,7 +47,7 @@ git diff --name-only
 6. Commit and merge back to base using guardex finish flow:
 
 ```sh
-git add .codex/skills templates/codex/skills
+git add skills .codex/skills templates/codex/skills
 git commit -m "Merge skill file updates into ${BASE_BRANCH}"
 gx branch finish --branch "$(git rev-parse --abbrev-ref HEAD)" --base "$BASE_BRANCH" --via-pr --wait-for-merge --cleanup
 ```

package/templates/scripts/agent-branch-finish.sh

@@ -15,6 +15,7 @@ CLEANUP_AFTER_MERGE_RAW="${GUARDEX_FINISH_CLEANUP:-false}"
 WAIT_FOR_MERGE_RAW="${GUARDEX_FINISH_WAIT_FOR_MERGE:-false}"
 WAIT_TIMEOUT_SECONDS_RAW="${GUARDEX_FINISH_WAIT_TIMEOUT_SECONDS:-1800}"
 WAIT_POLL_SECONDS_RAW="${GUARDEX_FINISH_WAIT_POLL_SECONDS:-10}"
+PARENT_GITLINK_AUTO_COMMIT_RAW="${GUARDEX_FINISH_PARENT_GITLINK_AUTO_COMMIT:-true}"
 
 run_guardex_cli() {
   if [[ -n "$CLI_ENTRY" ]]; then
@@ -67,6 +68,7 @@ CLEANUP_AFTER_MERGE="$(normalize_bool "$CLEANUP_AFTER_MERGE_RAW" "0")"
 WAIT_FOR_MERGE="$(normalize_bool "$WAIT_FOR_MERGE_RAW" "0")"
 WAIT_TIMEOUT_SECONDS="$(normalize_int "$WAIT_TIMEOUT_SECONDS_RAW" "1800" "30")"
 WAIT_POLL_SECONDS="$(normalize_int "$WAIT_POLL_SECONDS_RAW" "10" "0")"
+PARENT_GITLINK_AUTO_COMMIT="$(normalize_bool "$PARENT_GITLINK_AUTO_COMMIT_RAW" "1")"
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
@@ -117,6 +119,14 @@ while [[ $# -gt 0 ]]; do
       WAIT_POLL_SECONDS="$(normalize_int "${2:-}" "10" "0")"
       shift 2
       ;;
+    --parent-gitlink-commit)
+      PARENT_GITLINK_AUTO_COMMIT=1
+      shift
+      ;;
+    --no-parent-gitlink-commit)
+      PARENT_GITLINK_AUTO_COMMIT=0
+      shift
+      ;;
     --mode)
       MERGE_MODE="${2:-auto}"
       shift 2
@@ -131,7 +141,7 @@ while [[ $# -gt 0 ]]; do
       ;;
     *)
       echo "[agent-branch-finish] Unknown argument: $1" >&2
-      echo "Usage: $0 [--base <branch>] [--branch <branch>] [--no-push] [--cleanup|--no-cleanup] [--wait-for-merge|--no-wait-for-merge] [--wait-timeout-seconds <n>] [--wait-poll-seconds <n>] [--keep-remote-branch|--delete-remote-branch] [--mode auto|direct|pr|--via-pr|--direct-only]" >&2
+      echo "Usage: $0 [--base <branch>] [--branch <branch>] [--no-push] [--cleanup|--no-cleanup] [--wait-for-merge|--no-wait-for-merge] [--wait-timeout-seconds <n>] [--wait-poll-seconds <n>] [--parent-gitlink-commit|--no-parent-gitlink-commit] [--keep-remote-branch|--delete-remote-branch] [--mode auto|direct|pr|--via-pr|--direct-only]" >&2
       exit 1
       ;;
   esac
@@ -173,6 +183,8 @@ if [[ -z "$stored_worktree_root_rel" ]]; then
   stored_worktree_root_rel=".omx/agent-worktrees"
 fi
 agent_worktree_root="${repo_common_root}/${stored_worktree_root_rel}"
+runtime_state_root_rel="$(dirname "$stored_worktree_root_rel")"
+temp_worktree_root="${repo_common_root}/${runtime_state_root_rel}/.tmp-worktrees"
 
 if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 && -z "$BASE_BRANCH" ]]; then
   echo "[agent-branch-finish] --base requires a non-empty branch name." >&2
@@ -218,7 +230,7 @@ fi
 
 get_worktree_for_branch() {
   local branch="$1"
-  git -C "$repo_root" worktree list --porcelain | awk -v target="refs/heads/${branch}" -v probe_prefix="${agent_worktree_root}/__source-probe-" '
+  git -C "$repo_root" worktree list --porcelain | awk -v target="refs/heads/${branch}" -v probe_prefix="${temp_worktree_root}/__source-probe-" '
     $1 == "worktree" { wt = $2 }
     $1 == "branch" && $2 == target {
       if (index(wt, probe_prefix) != 1) {
@@ -242,7 +254,7 @@ remove_stale_source_probe_worktrees() {
     git -C "$stale_probe" merge --abort >/dev/null 2>&1 || true
     git -C "$repo_root" worktree remove "$stale_probe" --force >/dev/null 2>&1 || true
   done < <(
-    git -C "$repo_root" worktree list --porcelain | awk -v target="refs/heads/${branch}" -v probe_prefix="${agent_worktree_root}/__source-probe-" '
+    git -C "$repo_root" worktree list --porcelain | awk -v target="refs/heads/${branch}" -v probe_prefix="${temp_worktree_root}/__source-probe-" '
       $1 == "worktree" { wt = $2 }
       $1 == "branch" && $2 == target {
         if (index(wt, probe_prefix) == 1) {
@@ -264,11 +276,15 @@ source_worktree="$(get_worktree_for_branch "$SOURCE_BRANCH")"
 created_source_probe=0
 source_probe_path=""
 integration_worktree=""
+integration_branch=""
 
 cleanup() {
   if [[ -n "$integration_worktree" && -d "$integration_worktree" ]]; then
     git -C "$repo_root" worktree remove "$integration_worktree" --force >/dev/null 2>&1 || true
   fi
+  if [[ -n "${integration_branch:-}" ]]; then
+    git -C "$repo_root" branch -D "$integration_branch" >/dev/null 2>&1 || true
+  fi
   if [[ "$created_source_probe" -eq 1 && -n "$source_probe_path" && -d "$source_probe_path" ]]; then
     # Abort any in-progress git op so `worktree remove --force` succeeds on conflict-stuck probes.
     git -C "$source_probe_path" rebase --abort >/dev/null 2>&1 || true
@@ -279,7 +295,7 @@ cleanup() {
 trap cleanup EXIT
 
 if [[ -z "$source_worktree" ]]; then
-  source_probe_path="${agent_worktree_root}/__source-probe-${SOURCE_BRANCH//\//__}-$(date +%Y%m%d-%H%M%S)"
+  source_probe_path="${temp_worktree_root}/__source-probe-${SOURCE_BRANCH//\//__}-$(date +%Y%m%d-%H%M%S)"
   mkdir -p "$(dirname "$source_probe_path")"
   git -C "$repo_root" worktree add "$source_probe_path" "$SOURCE_BRANCH" >/dev/null
   source_worktree="$source_probe_path"
@@ -343,7 +359,7 @@ if [[ "$should_require_sync" -eq 1 ]] && git -C "$repo_root" show-ref --verify -
 fi
 
 integration_stamp="$(date +%Y%m%d-%H%M%S)"
-integration_worktree_base="${agent_worktree_root}/__integrate-${BASE_BRANCH//\//__}-${integration_stamp}"
+integration_worktree_base="${temp_worktree_root}/__integrate-${BASE_BRANCH//\//__}-${integration_stamp}"
 integration_branch_base="__agent_integrate_${BASE_BRANCH//\//_}_$(date +%Y%m%d_%H%M%S)"
 integration_worktree="$integration_worktree_base"
 integration_branch="$integration_branch_base"
@@ -493,6 +509,90 @@ read_merged_pr_for_head() {
   return 0
 }
 
+maybe_auto_commit_parent_gitlink() {
+  local base_wt="${1:-}"
+  local base_wt_real=""
+  local super_root_raw=""
+  local super_root=""
+  local subrepo_rel=""
+  local gitlink_mode=""
+  local gitlink_index_sha=""
+  local gitlink_parent_head_sha=""
+  local subrepo_head_sha=""
+  local update_index_output=""
+  local commit_output=""
+  local commit_message=""
+
+  if [[ "$PARENT_GITLINK_AUTO_COMMIT" -ne 1 || "$PUSH_ENABLED" -ne 1 ]]; then
+    return 0
+  fi
+  if [[ -z "$base_wt" ]]; then
+    return 0
+  fi
+  if ! base_wt_real="$(cd "$base_wt" && pwd -P 2>/dev/null)"; then
+    return 0
+  fi
+  if [[ "$base_wt_real" != "$repo_common_root" ]]; then
+    return 0
+  fi
+  if ! is_clean_worktree "$repo_common_root"; then
+    echo "[agent-branch-finish] Parent gitlink auto-commit skipped; nested base worktree is dirty: ${repo_common_root}" >&2
+    return 0
+  fi
+
+  super_root_raw="$(git -C "$repo_common_root" rev-parse --show-superproject-working-tree 2>/dev/null || true)"
+  if [[ -z "$super_root_raw" ]]; then
+    return 0
+  fi
+  if ! super_root="$(cd "$super_root_raw" && pwd -P 2>/dev/null)"; then
+    return 0
+  fi
+
+  case "$repo_common_root" in
+    "$super_root"/*) subrepo_rel="${repo_common_root#"$super_root"/}" ;;
+    *) return 0 ;;
+  esac
+  if [[ -z "$subrepo_rel" || "$subrepo_rel" == "$repo_common_root" ]]; then
+    return 0
+  fi
+
+  gitlink_mode="$(git -C "$super_root" ls-files -s -- "$subrepo_rel" | awk 'NR == 1 { print $1 }')"
+  if [[ "$gitlink_mode" != "160000" ]]; then
+    return 0
+  fi
+  gitlink_index_sha="$(git -C "$super_root" ls-files -s -- "$subrepo_rel" | awk 'NR == 1 { print $2 }')"
+  gitlink_parent_head_sha="$(git -C "$super_root" ls-tree HEAD -- "$subrepo_rel" | awk 'NR == 1 { print $3 }')"
+  subrepo_head_sha="$(git -C "$repo_common_root" rev-parse HEAD 2>/dev/null || true)"
+  if [[ -z "$subrepo_head_sha" ]]; then
+    return 0
+  fi
+  if [[ -n "$gitlink_index_sha" && "$gitlink_index_sha" == "$gitlink_parent_head_sha" && "$gitlink_index_sha" == "$subrepo_head_sha" ]]; then
+    return 0
+  fi
+
+  if [[ "$gitlink_index_sha" != "$subrepo_head_sha" ]]; then
+    if ! update_index_output="$(git -C "$super_root" update-index --cacheinfo 160000 "$subrepo_head_sha" "$subrepo_rel" 2>&1)"; then
+      echo "[agent-branch-finish] Warning: parent gitlink staging failed for ${subrepo_rel} in ${super_root}." >&2
+      [[ -n "$update_index_output" ]] && echo "$update_index_output" >&2
+      return 0
+    fi
+    gitlink_index_sha="$(git -C "$super_root" ls-files -s -- "$subrepo_rel" | awk 'NR == 1 { print $2 }')"
+  fi
+  gitlink_parent_head_sha="$(git -C "$super_root" ls-tree HEAD -- "$subrepo_rel" | awk 'NR == 1 { print $3 }')"
+  if [[ "$gitlink_index_sha" == "$gitlink_parent_head_sha" ]]; then
+    return 0
+  fi
+
+  commit_message="Update ${subrepo_rel} subrepo pointer"
+  if ! commit_output="$(git -C "$super_root" commit -m "$commit_message" -- "$subrepo_rel" 2>&1)"; then
+    echo "[agent-branch-finish] Warning: parent gitlink auto-commit failed in ${super_root}." >&2
+    [[ -n "$commit_output" ]] && echo "$commit_output" >&2
+    return 0
+  fi
+
+  echo "[agent-branch-finish] Parent gitlink auto-committed '${subrepo_rel}' in ${super_root}."
+}
+
 wait_for_pr_merge() {
   local deadline
   deadline=$(( $(date +%s) + WAIT_TIMEOUT_SECONDS ))
@@ -661,6 +761,7 @@ base_worktree="$(get_worktree_for_branch "$BASE_BRANCH")"
 if [[ -n "$base_worktree" ]] && is_clean_worktree "$base_worktree" && [[ "$PUSH_ENABLED" -eq 1 ]]; then
   git -C "$base_worktree" pull --ff-only origin "$BASE_BRANCH" >/dev/null 2>&1 || true
 fi
+maybe_auto_commit_parent_gitlink "$base_worktree"
 
 if [[ "$CLEANUP_AFTER_MERGE" -eq 1 ]]; then
   if [[ "$source_worktree" == "$repo_root" ]]; then

package/templates/scripts/agent-worktree-prune.sh

@@ -20,7 +20,9 @@ PR_MERGED_LOOKUP_LOADED=0
 declare -A MERGED_PR_BRANCHES=()
 WORKTREE_ROOT_RELS=(
   ".omx/agent-worktrees"
+  ".omx/.tmp-worktrees"
   ".omc/agent-worktrees"
+  ".omc/.tmp-worktrees"
 )
 
 if [[ -n "$BASE_BRANCH" ]]; then
@@ -90,9 +92,15 @@ repo_common_dir="$(cd "$repo_common_dir" && pwd -P)"
 resolve_worktree_root_rel_for_entry() {
   local entry="$1"
   case "$entry" in
+    */.omc/.tmp-worktrees/*)
+      printf '%s' '.omc/.tmp-worktrees'
+      ;;
     */.omc/agent-worktrees/*)
       printf '%s' '.omc/agent-worktrees'
       ;;
+    */.omx/.tmp-worktrees/*)
+      printf '%s' '.omx/.tmp-worktrees'
+      ;;
     *)
       printf '%s' '.omx/agent-worktrees'
       ;;
@@ -538,6 +546,19 @@ if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
     if branch_has_worktree "$branch"; then
       continue
     fi
+    if [[ "$branch" == __agent_integrate_* || "$branch" == __source-probe-* ]]; then
+      if ! branch_idle_gate "$branch" "" "temporary-worktree"; then
+        continue
+      fi
+      if run_cmd git -C "$repo_root" branch -D "$branch" >/dev/null 2>&1; then
+        removed_branches=$((removed_branches + 1))
+        echo "[agent-worktree-prune] Deleted stale temporary branch: ${branch}"
+      fi
+      continue
+    fi
+    if [[ "$branch" != agent/* ]]; then
+      continue
+    fi
     if ! branch_idle_gate "$branch" "" "stale-merged-branch"; then
       continue
     fi
@@ -566,7 +587,7 @@ if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
         fi
       fi
     fi
-  done < <(git -C "$repo_root" for-each-ref --format='%(refname:short)' refs/heads/agent)
+  done < <(git -C "$repo_root" for-each-ref --format='%(refname:short)' refs/heads)
 fi
 
 run_cmd git -C "$repo_root" worktree prune