diff --git a/AGENTS.md b/AGENTS.md
index 1b3c98e..2910a4f 100644
--- a/AGENTS.md
+++ b/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
    ```
diff --git a/README.md b/README.md
index 6c8a5ae..d335e89 100644
--- a/README.md
+++ b/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
 ```
 
diff --git a/bin/multiagent-safety.js b/bin/multiagent-safety.js
index 68d4933..bf1c671 100755
--- a/bin/multiagent-safety.js
+++ b/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) {
diff --git a/openspec/changes/agent-codex-split-claude-worktrees-under-omc-2026-04-21-13-46/notes.md b/openspec/changes/agent-codex-split-claude-worktrees-under-omc-2026-04-21-13-46/notes.md
new file mode 100644
index 0000000..3ea1120
--- /dev/null
+++ b/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.
diff --git a/scripts/agent-branch-finish.sh b/scripts/agent-branch-finish.sh
index 95ee231..fb528e1 100755
--- a/scripts/agent-branch-finish.sh
+++ b/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
diff --git a/scripts/agent-branch-start.sh b/scripts/agent-branch-start.sh
index e56e376..7e3024b 100755
--- a/scripts/agent-branch-start.sh
+++ b/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
 
diff --git a/scripts/agent-worktree-prune.sh b/scripts/agent-worktree-prune.sh
index 0644ba1..c967140 100755
--- a/scripts/agent-worktree-prune.sh
+++ b/scripts/agent-worktree-prune.sh
@@ -18,6 +18,10 @@ GH_BIN="${GUARDEX_GH_BIN:-gh}"
 PR_MERGED_LOOKUP_DISABLED=0
 PR_MERGED_LOOKUP_LOADED=0
 declare -A MERGED_PR_BRANCHES=()
+WORKTREE_ROOT_RELS=(
+  ".omx/agent-worktrees"
+  ".omc/agent-worktrees"
+)
 
 if [[ -n "$BASE_BRANCH" ]]; then
   BASE_BRANCH_EXPLICIT=1
@@ -77,13 +81,36 @@ fi
 
 repo_root="$(git rev-parse --show-toplevel)"
 current_pwd="$(pwd -P)"
-worktree_root="${repo_root}/.omx/agent-worktrees"
 repo_common_dir="$(
   git -C "$repo_root" rev-parse --git-common-dir \
     | awk -v root="$repo_root" '{ if ($0 ~ /^\//) { print $0 } else { print root "/" $0 } }'
 )"
 repo_common_dir="$(cd "$repo_common_dir" && pwd -P)"
 
+resolve_worktree_root_rel_for_entry() {
+  local entry="$1"
+  case "$entry" in
+    */.omc/agent-worktrees/*)
+      printf '%s' '.omc/agent-worktrees'
+      ;;
+    *)
+      printf '%s' '.omx/agent-worktrees'
+      ;;
+  esac
+}
+
+is_managed_worktree_path() {
+  local entry="$1"
+  local rel root
+  for rel in "${WORKTREE_ROOT_RELS[@]}"; do
+    root="${repo_root}/${rel}"
+    if [[ "$entry" == "${root}"/* ]]; then
+      return 0
+    fi
+  done
+  return 1
+}
+
 resolve_base_branch() {
   local configured=""
   local current=""
@@ -308,54 +335,59 @@ relocated_foreign=0
 skipped_foreign=0
 
 relocate_foreign_worktree_entries() {
-  [[ -d "$worktree_root" ]] || return 0
-
-  local entry=""
-  for entry in "${worktree_root}"/*; do
-    [[ -d "$entry" ]] || continue
-    if ! git -C "$entry" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-      continue
-    fi
-
-    local entry_common_dir=""
-    entry_common_dir="$(resolve_worktree_common_dir "$entry" || true)"
-    [[ -n "$entry_common_dir" ]] || continue
+  local rel="" worktree_root="" entry=""
+  for rel in "${WORKTREE_ROOT_RELS[@]}"; do
+    worktree_root="${repo_root}/${rel}"
+    [[ -d "$worktree_root" ]] || continue
+
+    for entry in "${worktree_root}"/*; do
+      [[ -d "$entry" ]] || continue
+      if ! git -C "$entry" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+        continue
+      fi
 
-    if [[ "$entry_common_dir" == "$repo_common_dir" ]]; then
-      continue
-    fi
+      local entry_common_dir=""
+      entry_common_dir="$(resolve_worktree_common_dir "$entry" || true)"
+      [[ -n "$entry_common_dir" ]] || continue
 
-    if [[ "$(basename "$entry_common_dir")" != ".git" ]]; then
-      skipped_foreign=$((skipped_foreign + 1))
-      echo "[agent-worktree-prune] Skipping foreign worktree with unsupported git common dir: ${entry}"
-      continue
-    fi
+      if [[ "$entry_common_dir" == "$repo_common_dir" ]]; then
+        continue
+      fi
 
-    local owner_repo_root
-    owner_repo_root="$(dirname "$entry_common_dir")"
-    local owner_worktree_root="${owner_repo_root}/.omx/agent-worktrees"
-    local target_path
-    target_path="$(select_unique_worktree_path "$owner_worktree_root" "$(basename "$entry")")"
+      if [[ "$(basename "$entry_common_dir")" != ".git" ]]; then
+        skipped_foreign=$((skipped_foreign + 1))
+        echo "[agent-worktree-prune] Skipping foreign worktree with unsupported git common dir: ${entry}"
+        continue
+      fi
 
-    if [[ "$entry" == "$current_pwd" || "$current_pwd" == "${entry}"/* ]]; then
-      skipped_foreign=$((skipped_foreign + 1))
-      echo "[agent-worktree-prune] Skipping active foreign worktree: ${entry}"
-      continue
-    fi
+      local owner_repo_root
+      owner_repo_root="$(dirname "$entry_common_dir")"
+      local owner_worktree_root_rel owner_worktree_root
+      owner_worktree_root_rel="$(resolve_worktree_root_rel_for_entry "$entry")"
+      owner_worktree_root="${owner_repo_root}/${owner_worktree_root_rel}"
+      local target_path
+      target_path="$(select_unique_worktree_path "$owner_worktree_root" "$(basename "$entry")")"
+
+      if [[ "$entry" == "$current_pwd" || "$current_pwd" == "${entry}"/* ]]; then
+        skipped_foreign=$((skipped_foreign + 1))
+        echo "[agent-worktree-prune] Skipping active foreign worktree: ${entry}"
+        continue
+      fi
 
-    echo "[agent-worktree-prune] Relocating foreign worktree to owning repo: ${entry} -> ${target_path}"
-    if [[ "$DRY_RUN" -eq 1 ]]; then
-      relocated_foreign=$((relocated_foreign + 1))
-      continue
-    fi
+      echo "[agent-worktree-prune] Relocating foreign worktree to owning repo: ${entry} -> ${target_path}"
+      if [[ "$DRY_RUN" -eq 1 ]]; then
+        relocated_foreign=$((relocated_foreign + 1))
+        continue
+      fi
 
-    mkdir -p "$owner_worktree_root"
-    if git -C "$owner_repo_root" worktree move "$entry" "$target_path" >/dev/null 2>&1; then
-      relocated_foreign=$((relocated_foreign + 1))
-    else
-      skipped_foreign=$((skipped_foreign + 1))
-      echo "[agent-worktree-prune] Failed to relocate foreign worktree: ${entry}" >&2
-    fi
+      mkdir -p "$owner_worktree_root"
+      if git -C "$owner_repo_root" worktree move "$entry" "$target_path" >/dev/null 2>&1; then
+        relocated_foreign=$((relocated_foreign + 1))
+      else
+        skipped_foreign=$((skipped_foreign + 1))
+        echo "[agent-worktree-prune] Failed to relocate foreign worktree: ${entry}" >&2
+      fi
+    done
   done
 }
 
@@ -371,7 +403,9 @@ process_entry() {
   local branch_ref="$2"
 
   [[ -z "$wt" ]] && return
-  [[ "$wt" != "${worktree_root}"/* ]] && return
+  if ! is_managed_worktree_path "$wt"; then
+    return
+  fi
 
   local branch=""
   if [[ -n "$branch_ref" ]]; then
diff --git a/templates/scripts/agent-branch-finish.sh b/templates/scripts/agent-branch-finish.sh
index 95ee231..fb528e1 100755
--- a/templates/scripts/agent-branch-finish.sh
+++ b/templates/scripts/agent-branch-finish.sh
@@ -144,12 +144,17 @@ else
   common_git_dir="$(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
diff --git a/templates/scripts/agent-branch-start.sh b/templates/scripts/agent-branch-start.sh
index e56e376..7e3024b 100755
--- a/templates/scripts/agent-branch-start.sh
+++ b/templates/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
 
diff --git a/templates/scripts/agent-worktree-prune.sh b/templates/scripts/agent-worktree-prune.sh
index 0644ba1..c967140 100644
--- a/templates/scripts/agent-worktree-prune.sh
+++ b/templates/scripts/agent-worktree-prune.sh
@@ -18,6 +18,10 @@ GH_BIN="${GUARDEX_GH_BIN:-gh}"
 PR_MERGED_LOOKUP_DISABLED=0
 PR_MERGED_LOOKUP_LOADED=0
 declare -A MERGED_PR_BRANCHES=()
+WORKTREE_ROOT_RELS=(
+  ".omx/agent-worktrees"
+  ".omc/agent-worktrees"
+)
 
 if [[ -n "$BASE_BRANCH" ]]; then
   BASE_BRANCH_EXPLICIT=1
@@ -77,13 +81,36 @@ fi
 
 repo_root="$(git rev-parse --show-toplevel)"
 current_pwd="$(pwd -P)"
-worktree_root="${repo_root}/.omx/agent-worktrees"
 repo_common_dir="$(
   git -C "$repo_root" rev-parse --git-common-dir \
     | awk -v root="$repo_root" '{ if ($0 ~ /^\//) { print $0 } else { print root "/" $0 } }'
 )"
 repo_common_dir="$(cd "$repo_common_dir" && pwd -P)"
 
+resolve_worktree_root_rel_for_entry() {
+  local entry="$1"
+  case "$entry" in
+    */.omc/agent-worktrees/*)
+      printf '%s' '.omc/agent-worktrees'
+      ;;
+    *)
+      printf '%s' '.omx/agent-worktrees'
+      ;;
+  esac
+}
+
+is_managed_worktree_path() {
+  local entry="$1"
+  local rel root
+  for rel in "${WORKTREE_ROOT_RELS[@]}"; do
+    root="${repo_root}/${rel}"
+    if [[ "$entry" == "${root}"/* ]]; then
+      return 0
+    fi
+  done
+  return 1
+}
+
 resolve_base_branch() {
   local configured=""
   local current=""
@@ -308,54 +335,59 @@ relocated_foreign=0
 skipped_foreign=0
 
 relocate_foreign_worktree_entries() {
-  [[ -d "$worktree_root" ]] || return 0
-
-  local entry=""
-  for entry in "${worktree_root}"/*; do
-    [[ -d "$entry" ]] || continue
-    if ! git -C "$entry" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-      continue
-    fi
-
-    local entry_common_dir=""
-    entry_common_dir="$(resolve_worktree_common_dir "$entry" || true)"
-    [[ -n "$entry_common_dir" ]] || continue
+  local rel="" worktree_root="" entry=""
+  for rel in "${WORKTREE_ROOT_RELS[@]}"; do
+    worktree_root="${repo_root}/${rel}"
+    [[ -d "$worktree_root" ]] || continue
+
+    for entry in "${worktree_root}"/*; do
+      [[ -d "$entry" ]] || continue
+      if ! git -C "$entry" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+        continue
+      fi
 
-    if [[ "$entry_common_dir" == "$repo_common_dir" ]]; then
-      continue
-    fi
+      local entry_common_dir=""
+      entry_common_dir="$(resolve_worktree_common_dir "$entry" || true)"
+      [[ -n "$entry_common_dir" ]] || continue
 
-    if [[ "$(basename "$entry_common_dir")" != ".git" ]]; then
-      skipped_foreign=$((skipped_foreign + 1))
-      echo "[agent-worktree-prune] Skipping foreign worktree with unsupported git common dir: ${entry}"
-      continue
-    fi
+      if [[ "$entry_common_dir" == "$repo_common_dir" ]]; then
+        continue
+      fi
 
-    local owner_repo_root
-    owner_repo_root="$(dirname "$entry_common_dir")"
-    local owner_worktree_root="${owner_repo_root}/.omx/agent-worktrees"
-    local target_path
-    target_path="$(select_unique_worktree_path "$owner_worktree_root" "$(basename "$entry")")"
+      if [[ "$(basename "$entry_common_dir")" != ".git" ]]; then
+        skipped_foreign=$((skipped_foreign + 1))
+        echo "[agent-worktree-prune] Skipping foreign worktree with unsupported git common dir: ${entry}"
+        continue
+      fi
 
-    if [[ "$entry" == "$current_pwd" || "$current_pwd" == "${entry}"/* ]]; then
-      skipped_foreign=$((skipped_foreign + 1))
-      echo "[agent-worktree-prune] Skipping active foreign worktree: ${entry}"
-      continue
-    fi
+      local owner_repo_root
+      owner_repo_root="$(dirname "$entry_common_dir")"
+      local owner_worktree_root_rel owner_worktree_root
+      owner_worktree_root_rel="$(resolve_worktree_root_rel_for_entry "$entry")"
+      owner_worktree_root="${owner_repo_root}/${owner_worktree_root_rel}"
+      local target_path
+      target_path="$(select_unique_worktree_path "$owner_worktree_root" "$(basename "$entry")")"
+
+      if [[ "$entry" == "$current_pwd" || "$current_pwd" == "${entry}"/* ]]; then
+        skipped_foreign=$((skipped_foreign + 1))
+        echo "[agent-worktree-prune] Skipping active foreign worktree: ${entry}"
+        continue
+      fi
 
-    echo "[agent-worktree-prune] Relocating foreign worktree to owning repo: ${entry} -> ${target_path}"
-    if [[ "$DRY_RUN" -eq 1 ]]; then
-      relocated_foreign=$((relocated_foreign + 1))
-      continue
-    fi
+      echo "[agent-worktree-prune] Relocating foreign worktree to owning repo: ${entry} -> ${target_path}"
+      if [[ "$DRY_RUN" -eq 1 ]]; then
+        relocated_foreign=$((relocated_foreign + 1))
+        continue
+      fi
 
-    mkdir -p "$owner_worktree_root"
-    if git -C "$owner_repo_root" worktree move "$entry" "$target_path" >/dev/null 2>&1; then
-      relocated_foreign=$((relocated_foreign + 1))
-    else
-      skipped_foreign=$((skipped_foreign + 1))
-      echo "[agent-worktree-prune] Failed to relocate foreign worktree: ${entry}" >&2
-    fi
+      mkdir -p "$owner_worktree_root"
+      if git -C "$owner_repo_root" worktree move "$entry" "$target_path" >/dev/null 2>&1; then
+        relocated_foreign=$((relocated_foreign + 1))
+      else
+        skipped_foreign=$((skipped_foreign + 1))
+        echo "[agent-worktree-prune] Failed to relocate foreign worktree: ${entry}" >&2
+      fi
+    done
   done
 }
 
@@ -371,7 +403,9 @@ process_entry() {
   local branch_ref="$2"
 
   [[ -z "$wt" ]] && return
-  [[ "$wt" != "${worktree_root}"/* ]] && return
+  if ! is_managed_worktree_path "$wt"; then
+    return
+  fi
 
   local branch=""
   if [[ -n "$branch_ref" ]]; then
diff --git a/test/install.test.js b/test/install.test.js
index 3c52ae5..a4eaa03 100644
--- a/test/install.test.js
+++ b/test/install.test.js
@@ -371,6 +371,8 @@ test('setup provisions workflow files and repo config', () => {
     '.omx/logs',
     '.omx/plans',
     '.omx/agent-worktrees',
+    '.omc',
+    '.omc/agent-worktrees',
     '.omx/notepad.md',
     '.omx/project-memory.json',
     'scripts/agent-branch-start.sh',
@@ -713,6 +715,7 @@ test('setup --parent-workspace-view creates one-level-up VS Code workspace for r
   assert.deepEqual(workspace.folders, [
     { path: path.basename(repoDir) },
     { path: `${path.basename(repoDir)}/.omx/agent-worktrees` },
+    { path: `${path.basename(repoDir)}/.omc/agent-worktrees` },
   ]);
   assert.equal(workspace.settings['scm.alwaysShowRepositories'], true);
 });
@@ -1129,6 +1132,8 @@ test('doctor on protected main bootstraps sandbox branch even before setup exist
   assert.equal(fs.existsSync(path.join(repoDir, '.omx', 'logs')), true);
   assert.equal(fs.existsSync(path.join(repoDir, '.omx', 'plans')), true);
   assert.equal(fs.existsSync(path.join(repoDir, '.omx', 'agent-worktrees')), true);
+  assert.equal(fs.existsSync(path.join(repoDir, '.omc')), true);
+  assert.equal(fs.existsSync(path.join(repoDir, '.omc', 'agent-worktrees')), true);
   assert.equal(fs.existsSync(path.join(repoDir, '.omx', 'notepad.md')), true);
   assert.equal(fs.existsSync(path.join(repoDir, '.omx', 'project-memory.json')), true);
 
@@ -1543,6 +1548,49 @@ test('setup agent-branch-start keeps role-datetime branch labels compact (v7.0.3
   assert.doesNotMatch(branchLeaf, /zeus|portasmosonma|admin-recodee/);
 });
 
+test('setup agent-branch-start routes Claude sessions into .omc worktrees and stores the selected root', () => {
+  const repoDir = initRepo();
+
+  let result = runNode(['setup', '--target', repoDir], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  seedCommit(repoDir);
+
+  result = runCmd(
+    'bash',
+    ['scripts/agent-branch-start.sh', 'claude-session-task', 'bot', 'dev'],
+    repoDir,
+    {
+      env: {
+        CLAUDECODE: '1',
+        GUARDEX_AGENT_TYPE: 'planner',
+      },
+    },
+  );
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const createdBranch = extractCreatedBranch(result.stdout);
+  assert.match(
+    createdBranch,
+    /^agent\/planner\/claude-session-task-\d{4}-\d{2}-\d{2}-\d{2}-\d{2}$/,
+  );
+
+  const createdWorktree = extractCreatedWorktree(result.stdout);
+  assert.match(
+    createdWorktree,
+    new RegExp(
+      `${escapeRegexLiteral(repoDir)}/\\.omc/agent-worktrees/${escapeRegexLiteral(createdBranch.replaceAll('/', '__'))}$`,
+    ),
+  );
+
+  const storedWorktreeRoot = runCmd(
+    'git',
+    ['config', '--get', `branch.${createdBranch}.guardexWorktreeRoot`],
+    repoDir,
+  );
+  assert.equal(storedWorktreeRoot.status, 0, storedWorktreeRoot.stderr || storedWorktreeRoot.stdout);
+  assert.equal(storedWorktreeRoot.stdout.trim(), '.omc/agent-worktrees');
+});
+
 test('setup agent-branch-start supports optional OpenSpec auto-bootstrap toggles', () => {
   const repoDir = initRepo();
 
@@ -1821,7 +1869,7 @@ test('agent-branch-start links dependency node_modules directories into new work
   }
 });
 
-test('agent-branch-finish infers base from source branch metadata and updates main worktree', () => {
+test('agent-branch-finish handles Claude-root worktrees when inferring base from source branch metadata', () => {
   const repoDir = initRepoOnBranch('main');
   seedCommit(repoDir);
   attachOriginRemoteForBranch(repoDir, 'main');
@@ -1837,10 +1885,13 @@ test('agent-branch-finish infers base from source branch metadata and updates ma
   result = runCmd('git', ['push', 'origin', 'main'], repoDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
 
-  result = runCmd('bash', ['scripts/agent-branch-start.sh', 'finish-from-dev', 'bot'], repoDir);
+  result = runCmd('bash', ['scripts/agent-branch-start.sh', 'finish-from-dev', 'bot'], repoDir, {
+    env: { CLAUDECODE: '1' },
+  });
   assert.equal(result.status, 0, result.stderr || result.stdout);
   const agentBranch = extractCreatedBranch(result.stdout);
   const agentWorktree = extractCreatedWorktree(result.stdout);
+  assert.match(agentWorktree, new RegExp(`${escapeRegexLiteral(repoDir)}/\\.omc/agent-worktrees/`));
 
   commitFile(agentWorktree, 'agent-finish-main.txt', 'merged via inferred main base\n', 'agent change for main');
 
@@ -3015,7 +3066,7 @@ test('codex-agent restores local branch and falls back to safe worktree start wh
   const combinedOutput = `${launch.stdout}\n${launch.stderr}`;
   assert.match(combinedOutput, /Unsafe starter output/);
   assert.match(combinedOutput, /\[agent-branch-start\] Created branch: agent\/planner\//);
-  assert.match(combinedOutput, /Origin remote does not provide a mergeable PR surface; skipping auto-finish merge\/PR pipeline/);
+  assert.match(combinedOutput, /\[codex-agent\] Auto-finish skipped.*no mergeable remote context/);
 
   const launchedCwd = fs.readFileSync(cwdMarker, 'utf8').trim();
   assert.match(