From 3624fd8d322fc192360c86a74e4af32354c3a316 Mon Sep 17 00:00:00 2001
From: NagyVikt <nagy.viktordp@gmail.com>
Date: Thu, 23 Apr 2026 11:57:28 +0200
Subject: [PATCH] Hide temporary finish helpers from visible agent worktrees

Finish helper worktrees were living under .omx/agent-worktrees and .omc/agent-worktrees, so VS Code surfaced __source-probe and __integrate repos beside real agent lanes. This moves those helpers into runtime-scoped .tmp-worktrees roots, deletes stale temporary refs at source and in prune sweeps, and extends scan-ignore/test coverage to keep the helper surface internal.

Constraint: Parent workspace view intentionally exposes .omx/agent-worktrees and .omc/agent-worktrees as real SCM lanes
Rejected: Keep helper worktrees under agent roots and only tweak labels | stale repos still surface in SCM and root scans
Confidence: high
Scope-risk: moderate
Reversibility: clean
Directive: Temporary finish helpers are internal-only; do not move them back under agent-worktrees without updating repo-scan ignores and prune behavior
Tested: bash -n scripts/agent-branch-finish.sh scripts/agent-worktree-prune.sh templates/scripts/agent-branch-finish.sh templates/scripts/agent-worktree-prune.sh; node --test test/finish.test.js test/worktree.test.js test/setup.test.js test/metadata.test.js; openspec validate agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56 --type change --strict
Not-tested: live GitHub PR finish flow on this manually created /tmp worktree lane
---
 .../proposal.md                               | 19 +++++++++
 .../temp-helper-worktree-cleanup/spec.md      | 41 +++++++++++++++++++
 .../tasks.md                                  | 26 ++++++++++++
 scripts/agent-branch-finish.sh                | 14 +++++--
 scripts/agent-worktree-prune.sh               | 23 ++++++++++-
 src/context.js                                |  4 ++
 templates/scripts/agent-branch-finish.sh      | 14 +++++--
 templates/scripts/agent-worktree-prune.sh     | 23 ++++++++++-
 test/finish.test.js                           |  4 +-
 test/helpers/install-test-helpers.js          |  4 ++
 test/setup.test.js                            |  4 ++
 test/worktree.test.js                         | 24 ++++++++++-
 12 files changed, 188 insertions(+), 12 deletions(-)
 create mode 100644 openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/proposal.md
 create mode 100644 openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/specs/temp-helper-worktree-cleanup/spec.md
 create mode 100644 openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/tasks.md

diff --git a/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/proposal.md b/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/proposal.md
new file mode 100644
index 00000000..240b8838
--- /dev/null
+++ b/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/proposal.md
@@ -0,0 +1,19 @@
+# Proposal: fix temp helper worktree cleanup
+
+## Why
+
+- `gx branch finish` creates `__source-probe-*` and `__integrate-*` helper worktrees under `.omx/agent-worktrees` / `.omc/agent-worktrees`, so VS Code surfaces them beside real agent lanes.
+- The finish flow removes temporary integration worktrees but can still leave stale `__agent_integrate_*` refs behind, which stacks up noisy helper branches after repeated doctor/finish runs.
+- Repo-level Git scan ignores currently cover only durable agent worktree roots, so moving helper worktrees into a dedicated internal temp root also needs settings parity.
+
+## What changes
+
+- Move temporary finish helpers into `.omx/.tmp-worktrees` and `.omc/.tmp-worktrees` instead of the user-visible agent worktree roots.
+- Delete temporary integration refs directly during finish cleanup and sweep any older stale temp refs in `gx cleanup`.
+- Extend managed VS Code repo-scan ignores and focused regressions for the new temp-helper placement and stale-temp-branch cleanup.
+
+## Scope
+
+- Affected runtime/scripts: `scripts/agent-branch-finish.sh`, `scripts/agent-worktree-prune.sh`
+- Affected template mirrors: `templates/scripts/*`
+- Affected config/test surface: `src/context.js`, `test/finish.test.js`, `test/worktree.test.js`, `test/setup.test.js`
diff --git a/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/specs/temp-helper-worktree-cleanup/spec.md b/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/specs/temp-helper-worktree-cleanup/spec.md
new file mode 100644
index 00000000..b06b02c5
--- /dev/null
+++ b/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/specs/temp-helper-worktree-cleanup/spec.md
@@ -0,0 +1,41 @@
+## ADDED Requirements
+
+### Requirement: finish helper worktrees stay outside durable agent roots
+
+`gx branch finish` SHALL create temporary `__source-probe-*` and `__integrate-*` helper worktrees under a runtime-scoped internal temp root (`.omx/.tmp-worktrees` for Codex lanes, `.omc/.tmp-worktrees` for Claude lanes) instead of the user-visible `.omx/agent-worktrees` or `.omc/agent-worktrees` roots.
+
+#### Scenario: Codex finish helper path stays outside `.omx/agent-worktrees`
+
+- **GIVEN** a Codex agent branch whose stored Guardex worktree root is `.omx/agent-worktrees`
+- **WHEN** `gx branch finish` creates a temporary source-probe or integration helper worktree
+- **THEN** the helper worktree path starts under `.omx/.tmp-worktrees`
+- **AND** the helper worktree path does not start under `.omx/agent-worktrees`
+
+#### Scenario: Claude finish helper path stays outside `.omc/agent-worktrees`
+
+- **GIVEN** a Claude agent branch whose stored Guardex worktree root is `.omc/agent-worktrees`
+- **WHEN** `gx branch finish` creates a temporary source-probe or integration helper worktree
+- **THEN** the helper worktree path starts under `.omc/.tmp-worktrees`
+- **AND** the helper worktree path does not start under `.omc/agent-worktrees`
+
+### Requirement: cleanup removes stale temporary helper refs
+
+`gx cleanup` and the finish exit path SHALL remove stale temporary helper refs (`__agent_integrate_*`, `__source-probe-*`) even when the matching helper worktree is already gone.
+
+#### Scenario: stale temporary integration ref is swept without a worktree
+
+- **GIVEN** a repo still has a local `__agent_integrate_*` branch ref
+- **AND** no worktree is attached to that ref anymore
+- **WHEN** `gx cleanup --delete-branches` runs
+- **THEN** the stale temporary ref is deleted
+
+### Requirement: repo scan ignores cover internal temp helper roots
+
+Guardex-managed VS Code repo scan ignores SHALL include `.omx/.tmp-worktrees` and `.omc/.tmp-worktrees` alongside the durable agent worktree roots.
+
+#### Scenario: setup appends temp helper roots to repo scan ignores
+
+- **GIVEN** `.vscode/settings.json` already has user-defined `git.repositoryScanIgnoredFolders`
+- **WHEN** `gx setup` or `gx doctor` refreshes the managed settings
+- **THEN** the existing user-defined entries remain
+- **AND** the resulting ignore list includes `.omx/.tmp-worktrees`, `**/.omx/.tmp-worktrees`, `.omc/.tmp-worktrees`, and `**/.omc/.tmp-worktrees`
diff --git a/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/tasks.md b/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/tasks.md
new file mode 100644
index 00000000..d859cbe3
--- /dev/null
+++ b/openspec/changes/agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56/tasks.md
@@ -0,0 +1,26 @@
+## 1. Spec
+
+- [x] 1.1 Define the helper-worktree placement and stale-temp-branch cleanup requirements.
+- [x] 1.2 Capture the scope in `proposal.md`.
+
+## 2. Tests
+
+- [x] 2.1 Update finish/worktree regressions for `.tmp-worktrees` helper paths and stale temp-ref cleanup.
+- [x] 2.2 Update setup expectations for the expanded repo-scan ignore list.
+
+## 3. Implementation
+
+- [x] 3.1 Move temporary finish helper worktrees into runtime-scoped `.tmp-worktrees` roots.
+- [x] 3.2 Delete temporary integration refs at finish exit and sweep stale helper refs in `gx cleanup`.
+- [x] 3.3 Extend repo scan ignore settings for temporary helper roots.
+
+## 4. Verification
+
+- [x] 4.1 Run focused tests for finish/prune/setup behavior.
+- [x] 4.2 Run `openspec validate agent-codex-fix-temp-helper-worktree-cleanup-2026-04-23-11-56 --type change --strict`.
+
+## 5. Cleanup
+
+- [ ] 5.1 Run `gx branch finish --branch agent/codex/fix-temp-helper-worktree-cleanup-2026-04-23-11-56 --base main --via-pr --wait-for-merge --cleanup`.
+- [ ] 5.2 Record PR URL + `MERGED` evidence.
+- [ ] 5.3 Confirm sandbox worktree and temp refs are gone (`git worktree list`, `git branch -a`).
diff --git a/scripts/agent-branch-finish.sh b/scripts/agent-branch-finish.sh
index 456abaec..400a08c1 100755
--- a/scripts/agent-branch-finish.sh
+++ b/scripts/agent-branch-finish.sh
@@ -173,6 +173,8 @@ 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 +220,7 @@ 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" && $2 == target {
       if (index(wt, probe_prefix) != 1) {
@@ -242,7 +244,7 @@ remove_stale_source_probe_worktrees() {
     git -C "$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" && $2 == target {
         if (index(wt, probe_prefix) == 1) {
@@ -264,11 +266,15 @@ source_worktree="$(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 +285,7 @@ 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="$source_probe_path"
@@ -343,7 +349,7 @@ if [[ "$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"
diff --git a/scripts/agent-worktree-prune.sh b/scripts/agent-worktree-prune.sh
index 1145fdc8..f039a912 100755
--- a/scripts/agent-worktree-prune.sh
+++ b/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 "$repo_root" worktree prune
diff --git a/src/context.js b/src/context.js
index cf2f21ce..2c931fec 100644
--- a/src/context.js
+++ b/src/context.js
@@ -263,8 +263,12 @@ const AGENT_WORKTREE_RELATIVE_DIRS = [
 const MANAGED_REPO_SCAN_IGNORED_FOLDERS = [
   '.omx/agent-worktrees',
   '**/.omx/agent-worktrees',
+  '.omx/.tmp-worktrees',
+  '**/.omx/.tmp-worktrees',
   '.omc/agent-worktrees',
   '**/.omc/agent-worktrees',
+  '.omc/.tmp-worktrees',
+  '**/.omc/.tmp-worktrees',
 ];
 const MANAGED_GITIGNORE_PATHS = [
   '.omx/',
diff --git a/templates/scripts/agent-branch-finish.sh b/templates/scripts/agent-branch-finish.sh
index 456abaec..400a08c1 100755
--- a/templates/scripts/agent-branch-finish.sh
+++ b/templates/scripts/agent-branch-finish.sh
@@ -173,6 +173,8 @@ if [[ -z "$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 +220,7 @@ 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" && $2 == target {
       if (index(wt, probe_prefix) != 1) {
@@ -242,7 +244,7 @@ remove_stale_source_probe_worktrees() {
     git -C "$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" && $2 == target {
         if (index(wt, probe_prefix) == 1) {
@@ -264,11 +266,15 @@ source_worktree="$(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 +285,7 @@ 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="$source_probe_path"
@@ -343,7 +349,7 @@ if [[ "$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"
diff --git a/templates/scripts/agent-worktree-prune.sh b/templates/scripts/agent-worktree-prune.sh
index 1145fdc8..f039a912 100644
--- a/templates/scripts/agent-worktree-prune.sh
+++ b/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
diff --git a/test/finish.test.js b/test/finish.test.js
index 07b39594..d40b3e63 100644
--- a/test/finish.test.js
+++ b/test/finish.test.js
@@ -224,7 +224,7 @@ test('agent-branch-finish removes stale source-probe worktrees before creating a
   const sourceProbePath = path.join(
     repoDir,
     '.omx',
-    'agent-worktrees',
+    '.tmp-worktrees',
     '__source-probe-agent__test-stale-source-probe-20260422-153300',
   );
   result = runCmd('git', ['worktree', 'add', sourceProbePath, 'agent/test-stale-source-probe'], repoDir);
@@ -235,6 +235,8 @@ test('agent-branch-finish removes stale source-probe worktrees before creating a
   assert.equal(finish.status, 0, finish.stderr || finish.stdout);
   assert.match(finish.stderr, /Removing stale source-probe worktree for 'agent\/test-stale-source-probe'/);
   assert.equal(fs.existsSync(sourceProbePath), false, 'stale source-probe worktree should be removed before finish continues');
+  result = runCmd('git', ['branch', '--list', '__agent_integrate_dev_*'], repoDir);
+  assert.equal(result.stdout.trim(), '', 'temporary integrate branches should be removed after finish exits');
   assert.match(
     finish.stdout,
     /Merged 'agent\/test-stale-source-probe' into 'dev' via direct flow and kept source branch\/worktree\./,
diff --git a/test/helpers/install-test-helpers.js b/test/helpers/install-test-helpers.js
index e10db744..8280df24 100644
--- a/test/helpers/install-test-helpers.js
+++ b/test/helpers/install-test-helpers.js
@@ -157,8 +157,12 @@ function assertManagedRepoVscodeSettings(settings) {
   assert.deepEqual(settings['git.repositoryScanIgnoredFolders'], [
     '.omx/agent-worktrees',
     '**/.omx/agent-worktrees',
+    '.omx/.tmp-worktrees',
+    '**/.omx/.tmp-worktrees',
     '.omc/agent-worktrees',
     '**/.omc/agent-worktrees',
+    '.omc/.tmp-worktrees',
+    '**/.omc/.tmp-worktrees',
   ]);
 }
 
diff --git a/test/setup.test.js b/test/setup.test.js
index bf951564..e3759bdf 100644
--- a/test/setup.test.js
+++ b/test/setup.test.js
@@ -1187,8 +1187,12 @@ test('setup merges Guardex repo-scan ignores into tracked VS Code workspace sett
     'custom-folder',
     '.omx/agent-worktrees',
     '**/.omx/agent-worktrees',
+    '.omx/.tmp-worktrees',
+    '**/.omx/.tmp-worktrees',
     '.omc/agent-worktrees',
     '**/.omc/agent-worktrees',
+    '.omc/.tmp-worktrees',
+    '**/.omc/.tmp-worktrees',
   ]);
 });
 
diff --git a/test/worktree.test.js b/test/worktree.test.js
index c91830ae..badc0a8f 100644
--- a/test/worktree.test.js
+++ b/test/worktree.test.js
@@ -151,7 +151,7 @@ test('worktree prune removes __source-probe worktrees even when they track agent
   const sourceProbePath = path.join(
     repoDir,
     '.omx',
-    'agent-worktrees',
+    '.tmp-worktrees',
     '__source-probe-agent__test-source-probe-prune-20260422-153300',
   );
   result = runCmd('git', ['worktree', 'add', sourceProbePath, 'agent/test-source-probe-prune'], repoDir);
@@ -167,6 +167,28 @@ test('worktree prune removes __source-probe worktrees even when they track agent
 });
 
 
+test('worktree prune deletes stale temporary helper branches without worktrees', () => {
+  const repoDir = initRepo();
+  let result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  seedCommit(repoDir);
+
+  result = runCmd('git', ['branch', '__agent_integrate_dev_20260423_114500', 'dev'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  result = runWorktreePrune(['--delete-branches'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  assert.match(result.stdout, /Deleted stale temporary branch: __agent_integrate_dev_20260423_114500/);
+
+  const branchResult = runCmd(
+    'git',
+    ['show-ref', '--verify', '--quiet', 'refs/heads/__agent_integrate_dev_20260423_114500'],
+    repoDir,
+  );
+  assert.notEqual(branchResult.status, 0, 'stale temporary helper branch should be removed');
+});
+
+
 test('worktree prune reroutes foreign worktrees to the owning repo .omx root', () => {
   const repoDir = initRepo();
   let result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);