Keep prune cleanup walking both managed worktree roots

AGENTS.md

@@ -87,12 +87,12 @@ bash scripts/agent-branch-start.sh "refactor-payment-pipeline" "claude-name"
    bash scripts/agent-branch-start.sh [--tier T0|T1|T2|T3] "<task>" "claude-<name>"
    ```
 
-   Creates `agent/claude-<name>/<slug>` under `.omx/agent-worktrees/`, scaffolds the OpenSpec change + plan workspaces (sized by tier), and records the bootstrap manifest. Missing `codex-auth` silently falls back to an empty snapshot slug (expected for Claude sessions).
+   Creates `agent/claude-<name>/<slug>` under `.omc/agent-worktrees/`, scaffolds the OpenSpec change + plan workspaces (sized by tier), and records the bootstrap manifest. Codex sessions keep using `.omx/agent-worktrees/`. Missing `codex-auth` silently falls back to an empty snapshot slug (expected for Claude sessions).
 
 2. Work inside the sandbox only:
 
    ```bash
-   cd .omx/agent-worktrees/agent__claude-<name>__<slug>
+   cd .omc/agent-worktrees/agent__claude-<name>__<slug>
    python3 scripts/agent-file-locks.py claim --branch "agent/claude-<name>/<slug>" <file...>
    # implement + commit inside this worktree
    ```

README.md

@@ -116,6 +116,8 @@ Running Codex across several existing worktrees (e.g. from VS Code Source Contro
 gx finish --all
 ```
 
+Codex sessions default to `.omx/agent-worktrees/`. Claude Code sessions default to `.omc/agent-worktrees/`, so Claude sandboxes stay under the Claude runtime folder instead of sharing the Codex root.
+
 ---
 
 ## Visual reference
@@ -161,7 +163,7 @@ gx setup --target /path/to/repo --parent-workspace-view
 
 ### Monorepo support
 
-Setup auto-installs into every nested git repo (e.g. `apps/*/.git`). Submodules and worktrees under `.omx/agent-worktrees/` are skipped.
+Setup auto-installs into every nested git repo (e.g. `apps/*/.git`). Submodules and worktrees under `.omx/agent-worktrees/` or `.omc/agent-worktrees/` are skipped.
 
 ```sh
 gx setup --target /mainfolder
@@ -460,6 +462,7 @@ scripts/openspec/init-plan-workspace.sh
 .claude/commands/gitguardex.md
 .github/pull.yml.example
 .github/workflows/cr.yml
+.omc/agent-worktrees
 .omx/state/agent-file-locks.json
 ```
 

bin/multiagent-safety.js

@@ -183,6 +183,12 @@ const AGENTS_MARKER_START = '<!-- multiagent-safety:START -->';
 const AGENTS_MARKER_END = '<!-- multiagent-safety:END -->';
 const GITIGNORE_MARKER_START = '# multiagent-safety:START';
 const GITIGNORE_MARKER_END = '# multiagent-safety:END';
+const CODEX_WORKTREE_RELATIVE_DIR = path.join('.omx', 'agent-worktrees');
+const CLAUDE_WORKTREE_RELATIVE_DIR = path.join('.omc', 'agent-worktrees');
+const AGENT_WORKTREE_RELATIVE_DIRS = [
+  CODEX_WORKTREE_RELATIVE_DIR,
+  CLAUDE_WORKTREE_RELATIVE_DIR,
+];
 const MANAGED_GITIGNORE_PATHS = [
   '.omx/',
   '.omc/',
@@ -202,7 +208,9 @@ const OMX_SCAFFOLD_DIRECTORIES = [
   '.omx/state',
   '.omx/logs',
   '.omx/plans',
-  '.omx/agent-worktrees',
+  CODEX_WORKTREE_RELATIVE_DIR,
+  '.omc',
+  CLAUDE_WORKTREE_RELATIVE_DIR,
 ];
 const OMX_SCAFFOLD_FILES = new Map([
   ['.omx/notepad.md', '\n\n## WORKING MEMORY\n'],
@@ -273,6 +281,19 @@ const AGENT_BOT_DESCRIPTIONS = [
   ['agents', 'Start/stop review + cleanup bots for this repo'],
 ];
 
+function envFlagIsTruthy(raw) {
+  const lowered = String(raw || '').trim().toLowerCase();
+  return lowered === '1' || lowered === 'true' || lowered === 'yes' || lowered === 'on';
+}
+
+function isClaudeCodeSession(env = process.env) {
+  return envFlagIsTruthy(env.CLAUDECODE) || Boolean(env.CLAUDE_CODE_SESSION_ID);
+}
+
+function defaultAgentWorktreeRelativeDir(env = process.env) {
+  return isClaudeCodeSession(env) ? CLAUDE_WORKTREE_RELATIVE_DIR : CODEX_WORKTREE_RELATIVE_DIR;
+}
+
 const AI_SETUP_PROMPT = `GitGuardex (gx) setup checklist for Codex/Claude in this repo.
 
 1) Install:    npm i -g @imdeadpool/guardex && gh --version
@@ -522,8 +543,6 @@ const NESTED_REPO_DEFAULT_SKIP_DIRS = new Set([
   '.venv',
   '.pnpm-store',
 ]);
-const NESTED_REPO_WORKTREE_RELATIVE_DIR = path.join('.omx', 'agent-worktrees');
-
 function discoverNestedGitRepos(rootPath, opts = {}) {
   const maxDepth = Number.isFinite(opts.maxDepth) ? Math.max(1, opts.maxDepth) : NESTED_REPO_DEFAULT_MAX_DEPTH;
   const extraSkip = new Set(Array.isArray(opts.extraSkip) ? opts.extraSkip : []);
@@ -538,7 +557,7 @@ function discoverNestedGitRepos(rootPath, opts = {}) {
     return path.resolve(resolvedRoot, raw);
   })();
 
-  const workreeSkipAbsolute = path.join(resolvedRoot, NESTED_REPO_WORKTREE_RELATIVE_DIR);
+  const worktreeSkipAbsolutes = AGENT_WORKTREE_RELATIVE_DIRS.map((relativeDir) => path.join(resolvedRoot, relativeDir));
   const found = new Set();
   found.add(resolvedRoot);
 
@@ -570,7 +589,7 @@ function discoverNestedGitRepos(rootPath, opts = {}) {
 
       if (!entry.isDirectory() || entry.isSymbolicLink()) continue;
       if (shouldSkipDir(entry.name)) continue;
-      if (entryPath === workreeSkipAbsolute) continue;
+      if (worktreeSkipAbsolutes.includes(entryPath)) continue;
       walk(entryPath, depth + 1);
     }
   }
@@ -1124,16 +1143,15 @@ function buildParentWorkspaceView(repoRoot) {
   const workspaceFileName = `${path.basename(repoRoot)}-branches.code-workspace`;
   const workspacePath = path.join(parentDir, workspaceFileName);
   const repoRelativePath = normalizeWorkspacePath(path.relative(parentDir, repoRoot) || '.');
-  const worktreesRelativePath = normalizeWorkspacePath(
-    path.join(repoRelativePath === '.' ? '' : repoRelativePath, '.omx', 'agent-worktrees'),
-  );
 
   return {
     workspacePath,
     payload: {
       folders: [
         { path: repoRelativePath },
-        { path: worktreesRelativePath },
+        ...AGENT_WORKTREE_RELATIVE_DIRS.map((relativeDir) => ({
+          path: normalizeWorkspacePath(path.join(repoRelativePath === '.' ? '' : repoRelativePath, relativeDir)),
+        })),
       ],
       settings: {
         'scm.alwaysShowRepositories': true,
@@ -1341,7 +1359,7 @@ function protectedBaseSandboxBranchPrefix() {
 }
 
 function protectedBaseSandboxWorktreePath(repoRoot, branchName) {
-  return path.join(repoRoot, '.omx', 'agent-worktrees', branchName.replace(/\//g, '__'));
+  return path.join(repoRoot, defaultAgentWorktreeRelativeDir(), branchName.replace(/\//g, '__'));
 }
 
 function gitRefExists(repoRoot, ref) {
@@ -1876,9 +1894,8 @@ function mergeDoctorSandboxRepairsBackToProtectedBase(options, blocked, metadata
       if (allowedPaths.has(filePath)) {
         return false;
       }
-      return !(
-        filePath === NESTED_REPO_WORKTREE_RELATIVE_DIR
-        || filePath.startsWith(`${NESTED_REPO_WORKTREE_RELATIVE_DIR}/`)
+      return !AGENT_WORKTREE_RELATIVE_DIRS.some(
+        (relativeDir) => filePath === relativeDir || filePath.startsWith(`${relativeDir}/`),
       );
     });
     if (unexpectedPaths.length > 0) {

openspec/changes/agent-codex-split-claude-worktrees-under-omc-2026-04-21-13-46/notes.md

@@ -0,0 +1,5 @@
+# T1 Notes
+
+- Route Claude-triggered Guardex worktrees into `.omc/agent-worktrees` by default while keeping Codex worktrees under `.omx/agent-worktrees`.
+- Persist the selected worktree root on each branch so `agent-branch-finish` and prune/recovery flows can resolve the correct sandbox root later.
+- Expand setup/workspace discovery, docs, and install regressions so nested-repo scans and VS Code parent-workspace views treat both `.omx` and `.omc` agent-worktree roots as managed paths.

scripts/agent-branch-finish.sh

@@ -144,12 +144,17 @@ else
   common_git_dir="$(cd "$repo_root/$common_git_dir_raw" && pwd -P)"
 fi
 repo_common_root="$(cd "$common_git_dir/.." && pwd -P)"
-agent_worktree_root="${repo_common_root}/.omx/agent-worktrees"
 
 if [[ -z "$SOURCE_BRANCH" ]]; then
   SOURCE_BRANCH="$(git rev-parse --abbrev-ref HEAD)"
 fi
 
+stored_worktree_root_rel="$(git -C "$repo_root" config --get "branch.${SOURCE_BRANCH}.guardexWorktreeRoot" || true)"
+if [[ -z "$stored_worktree_root_rel" ]]; then
+  stored_worktree_root_rel=".omx/agent-worktrees"
+fi
+agent_worktree_root="${repo_common_root}/${stored_worktree_root_rel}"
+
 if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 && -z "$BASE_BRANCH" ]]; then
   echo "[agent-branch-finish] --base requires a non-empty branch name." >&2
   exit 1

scripts/agent-branch-start.sh

@@ -5,7 +5,8 @@ TASK_NAME="task"
 AGENT_NAME="agent"
 BASE_BRANCH=""
 BASE_BRANCH_EXPLICIT=0
-WORKTREE_ROOT_REL=".omx/agent-worktrees"
+WORKTREE_ROOT_REL=""
+WORKTREE_ROOT_EXPLICIT=0
 OPENSPEC_AUTO_INIT_RAW="${GUARDEX_OPENSPEC_AUTO_INIT:-false}"
 OPENSPEC_PLAN_SLUG_OVERRIDE="${GUARDEX_OPENSPEC_PLAN_SLUG:-}"
 OPENSPEC_CHANGE_SLUG_OVERRIDE="${GUARDEX_OPENSPEC_CHANGE_SLUG:-}"
@@ -44,6 +45,7 @@ while [[ $# -gt 0 ]]; do
       ;;
     --worktree-root)
       WORKTREE_ROOT_REL="${2:-.omx/agent-worktrees}"
+      WORKTREE_ROOT_EXPLICIT=1
       shift 2
       ;;
     --)
@@ -123,6 +125,36 @@ shorten_slug() {
   printf '%s' "$shortened"
 }
 
+env_flag_truthy() {
+  local raw="${1:-}"
+  local lowered
+  lowered="$(printf '%s' "$raw" | tr '[:upper:]' '[:lower:]')"
+  case "$lowered" in
+    1|true|yes|on) return 0 ;;
+    *) return 1 ;;
+  esac
+}
+
+default_worktree_root_rel() {
+  local raw_agent="$1"
+  local override="${GUARDEX_AGENT_TYPE:-}"
+  local lowered_agent lowered_override
+  lowered_agent="$(printf '%s' "$raw_agent" | tr '[:upper:]' '[:lower:]')"
+  lowered_override="$(printf '%s' "$override" | tr '[:upper:]' '[:lower:]')"
+
+  if [[ -n "${CLAUDE_CODE_SESSION_ID:-}" ]] || env_flag_truthy "${CLAUDECODE:-}"; then
+    printf '.omc/agent-worktrees'
+    return 0
+  fi
+
+  if [[ "$lowered_agent" == *claude* ]] || [[ "$lowered_override" == *claude* ]]; then
+    printf '.omc/agent-worktrees'
+    return 0
+  fi
+
+  printf '.omx/agent-worktrees'
+}
+
 # Collapse arbitrary agent identifiers to a clean role token. Priority:
 # GUARDEX_AGENT_TYPE env override, then recognizable claude/codex aliases, then
 # a small legacy compatibility set, then the literal requested role after slug
@@ -415,6 +447,9 @@ fi
 
 task_slug="$(sanitize_slug "$TASK_NAME" "task")"
 agent_slug="$(normalize_role "$AGENT_NAME")"
+if [[ "$WORKTREE_ROOT_EXPLICIT" -eq 0 ]]; then
+  WORKTREE_ROOT_REL="$(default_worktree_root_rel "$AGENT_NAME")"
+fi
 branch_timestamp="$(compose_branch_timestamp)"
 branch_descriptor="$(compose_branch_descriptor "$task_slug" "$branch_timestamp")"
 branch_name_base="agent/${agent_slug}/${branch_descriptor}"
@@ -499,6 +534,7 @@ if ! worktree_add_output="$(git -C "$repo_root" worktree add -b "$branch_name" "
   exit 1
 fi
 git -C "$repo_root" config "branch.${branch_name}.guardexBase" "$BASE_BRANCH" >/dev/null 2>&1 || true
+git -C "$repo_root" config "branch.${branch_name}.guardexWorktreeRoot" "$WORKTREE_ROOT_REL" >/dev/null 2>&1 || true
 # Fresh agent branches should start unpublished; clear any inherited base-branch tracking.
 git -C "$worktree_path" branch --unset-upstream "$branch_name" >/dev/null 2>&1 || true