Stage parent gitlinks without status heuristics

openspec/changes/agent-codex-auto-commit-parent-subrepo-upgrades-2026-04-23-11-59/specs/finish/spec.md

@@ -10,7 +10,7 @@ After a successful nested repository finish, Guardex SHALL detect when the finis
 - **WHEN** `gx branch finish` merges the nested agent branch and fast-forwards the nested base worktree
 - **THEN** Guardex commits the parent repo gitlink path with a message naming that subrepo pointer
 - **AND** unrelated parent staged paths are not included in that commit
-- **AND** parent `diff.ignoreSubmodules=all` settings do not hide the gitlink pointer update from this detection
+- **AND** parent submodule ignore settings do not hide or prevent staging the gitlink pointer update
 
 #### Scenario: Parent auto-commit is disabled
 

openspec/changes/agent-codex-auto-commit-parent-subrepo-upgrades-2026-04-23-11-59/tasks.md

@@ -13,6 +13,7 @@
 - [x] Add parent gitlink detection and path-scoped parent commit to `agent-branch-finish`.
 - [x] Pass parent gitlink controls through `gx finish`.
 - [x] Compare gitlink index SHA to nested HEAD so parent `diff.ignoreSubmodules=all` does not hide pointer upgrades.
+- [x] Stage the gitlink with `git update-index --cacheinfo` so registered submodule ignore settings cannot suppress the pointer update.
 
 ## 4. Cleanup
 

scripts/agent-branch-finish.sh

@@ -519,7 +519,7 @@ maybe_auto_commit_parent_gitlink() {
   local gitlink_index_sha=""
   local gitlink_parent_head_sha=""
   local subrepo_head_sha=""
-  local add_output=""
+  local update_index_output=""
   local commit_output=""
   local commit_message=""
 
@@ -563,21 +563,24 @@ maybe_auto_commit_parent_gitlink() {
   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 "$repo_common_root" rev-parse HEAD 2>/dev/null || true)"
-  if [[ -n "$gitlink_index_sha" && "$gitlink_index_sha" == "$gitlink_parent_head_sha" && "$gitlink_index_sha" == "$subrepo_head_sha" ]]; then
+  if [[ -z "$subrepo_head_sha" ]]; then
     return 0
   fi
-
-  if ! add_output="$(git -C "$super_root" add -- "$subrepo_rel" 2>&1)"; then
-    echo "[agent-branch-finish] Warning: parent gitlink staging failed for ${subrepo_rel} in ${super_root}." >&2
-    [[ -n "$add_output" ]] && echo "$add_output" >&2
+  if [[ -n "$gitlink_index_sha" && "$gitlink_index_sha" == "$gitlink_parent_head_sha" && "$gitlink_index_sha" == "$subrepo_head_sha" ]]; then
     return 0
   fi
-  if git -C "$super_root" diff --cached --quiet -- "$subrepo_rel"; then
-    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 $3 }')"
-    if [[ "$gitlink_index_sha" == "$gitlink_parent_head_sha" ]]; then
+
+  if [[ "$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"

templates/scripts/agent-branch-finish.sh

@@ -519,7 +519,7 @@ maybe_auto_commit_parent_gitlink() {
   local gitlink_index_sha=""
   local gitlink_parent_head_sha=""
   local subrepo_head_sha=""
-  local add_output=""
+  local update_index_output=""
   local commit_output=""
   local commit_message=""
 
@@ -563,21 +563,24 @@ maybe_auto_commit_parent_gitlink() {
   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 "$repo_common_root" rev-parse HEAD 2>/dev/null || true)"
-  if [[ -n "$gitlink_index_sha" && "$gitlink_index_sha" == "$gitlink_parent_head_sha" && "$gitlink_index_sha" == "$subrepo_head_sha" ]]; then
+  if [[ -z "$subrepo_head_sha" ]]; then
     return 0
   fi
-
-  if ! add_output="$(git -C "$super_root" add -- "$subrepo_rel" 2>&1)"; then
-    echo "[agent-branch-finish] Warning: parent gitlink staging failed for ${subrepo_rel} in ${super_root}." >&2
-    [[ -n "$add_output" ]] && echo "$add_output" >&2
+  if [[ -n "$gitlink_index_sha" && "$gitlink_index_sha" == "$gitlink_parent_head_sha" && "$gitlink_index_sha" == "$subrepo_head_sha" ]]; then
     return 0
   fi
-  if git -C "$super_root" diff --cached --quiet -- "$subrepo_rel"; then
-    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 $3 }')"
-    if [[ "$gitlink_index_sha" == "$gitlink_parent_head_sha" ]]; then
+
+  if [[ "$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"

test/finish.test.js

@@ -190,6 +190,8 @@ test('agent-branch-finish auto-commits parent gitlink after nested repo finish',
   assert.equal(result.status, 0, result.stderr || result.stdout);
   result = runCmd('git', ['config', 'diff.ignoreSubmodules', 'all'], parentDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['config', 'submodule.packages/child.ignore', 'all'], parentDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
   fs.writeFileSync(path.join(parentDir, 'unrelated-parent.txt'), 'already staged\n', 'utf8');
   result = runCmd('git', ['add', 'unrelated-parent.txt'], parentDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);