diff --git a/README.md b/README.md
index c5f71be..eea933d 100644
--- a/README.md
+++ b/README.md
@@ -239,8 +239,9 @@ Use this exact checklist to setup multi-agent safety in this repository for Code
      start isolated agent branch/worktree -> claim file locks -> implement/verify ->
      finish via PR/merge cleanup with scripts/agent-branch-finish.sh.
    - `scripts/codex-agent.sh` now auto-runs this finish flow after Codex exits:
-     auto-commit changed files -> push/create PR -> merge attempt -> branch/worktree cleanup ->
-     pull local base branch.
+     auto-commit changed files -> push/create PR -> merge attempt -> keep branch/worktree for follow-up.
+   - Remove merged branches when you are done reviewing:
+     gx cleanup --branch "$(git rev-parse --abbrev-ref HEAD)"
 
 5) Optional: create OpenSpec planning workspace:
    bash scripts/openspec/init-plan-workspace.sh "<plan-slug>"
@@ -272,9 +273,11 @@ gx protect set <branch...> [--target <path>]
 gx protect reset [--target <path>]
 gx sync --check [--target <path>] [--base <branch>] [--json]
 gx sync [--target <path>] [--base <branch>] [--strategy rebase|merge] [--ff-only]
+gx cleanup [--target <path>] [--base <branch>] [--branch <agent/...>] [--dry-run] [--force-dirty] [--keep-remote]
 gx report scorecard [--target <path>] [--repo github.com/<owner>/<repo>] [--scorecard-json <file>] [--output-dir <path>] [--date YYYY-MM-DD]
-bash scripts/agent-worktree-prune.sh   # manual stale worktree cleanup (auto base detection)
-bash scripts/agent-worktree-prune.sh --force-dirty   # remove stale dirty worktrees too
+bash scripts/agent-worktree-prune.sh   # prune temporary worktrees only (keeps merged agent branches by default)
+bash scripts/agent-worktree-prune.sh --delete-branches --delete-remote-branches   # full merged-branch cleanup
+bash scripts/agent-worktree-prune.sh --force-dirty --delete-branches   # force-remove dirty merged worktrees too
 bash scripts/openspec/init-plan-workspace.sh <plan-slug>   # optional OpenSpec plan scaffold
 ```
 
@@ -291,8 +294,10 @@ and asks `[y/N]` whether to update immediately (default is `N`).
 - `gx doctor` on protected `main` auto-starts an isolated `agent/gx/...-gx-doctor` worktree branch and applies repairs there.
 - `gx setup` and `gx doctor` always refresh `.githooks/pre-commit` from templates, so Codex sub-branch enforcement stays repaired.
 - `scripts/codex-agent.sh` now auto-runs finish automation after a Codex session when `origin` exists:
-  auto-commit changed files, run PR/merge cleanup, and prune merged worktrees.
+  auto-commit changed files, run PR/merge automation, and keep merged agent branches/worktrees by default.
+  It also auto-syncs each sandbox branch against the latest base branch before task execution.
   If conflicts remain, it keeps the sandbox and prompts for a conflict-resolution review pass.
+- use `gx cleanup` (or `gx cleanup --branch <agent/...>`) to remove merged branches/worktrees when done.
 
 ## Advanced commands
 
diff --git a/bin/multiagent-safety.js b/bin/multiagent-safety.js
index b63f08b..37ab219 100755
--- a/bin/multiagent-safety.js
+++ b/bin/multiagent-safety.js
@@ -58,6 +58,8 @@ const CRITICAL_GUARDRAIL_PATHS = new Set([
   '.githooks/pre-commit',
   'scripts/agent-branch-start.sh',
   'scripts/agent-branch-finish.sh',
+  'scripts/agent-worktree-prune.sh',
+  'scripts/codex-agent.sh',
   'scripts/agent-file-locks.py',
 ]);
 
@@ -88,6 +90,7 @@ const COMMAND_TYPO_ALIASES = new Map([
   ['intsall', 'install'],
   ['docter', 'doctor'],
   ['doctro', 'doctor'],
+  ['cleunup', 'cleanup'],
   ['scna', 'scan'],
 ]);
 const SUGGESTIBLE_COMMANDS = [
@@ -100,6 +103,7 @@ const SUGGESTIBLE_COMMANDS = [
   'copy-commands',
   'protect',
   'sync',
+  'cleanup',
   'release',
   'install',
   'fix',
@@ -118,6 +122,7 @@ const CLI_COMMAND_DESCRIPTIONS = [
   ['copy-commands', 'Print setup checklist as executable commands only'],
   ['protect', 'Manage protected branches (list/add/remove/set/reset)'],
   ['sync', 'Check or sync agent branches with origin/<base>'],
+  ['cleanup', 'Cleanup merged agent branches/worktrees (local + remote)'],
   ['install', 'Install templates/locks/hooks without running full setup (supports --no-gitignore)'],
   ['fix', 'Repair broken or missing guardrail files/config (supports --no-gitignore)'],
   ['scan', 'Report safety issues and exit non-zero on findings'],
@@ -152,6 +157,9 @@ const AI_SETUP_PROMPT = `Use this exact checklist to setup GuardeX (Guardian T-R
    - For every new user message/task, repeat the same cycle:
      start isolated agent branch/worktree -> claim file locks -> implement/verify ->
      finish via PR/merge cleanup with scripts/agent-branch-finish.sh.
+   - Finished branches stay available by default for audit/follow-up.
+     Remove them explicitly when done:
+     gx cleanup --branch "$(git rev-parse --abbrev-ref HEAD)"
 
 5) Optional: create OpenSpec planning workspace:
    bash scripts/openspec/init-plan-workspace.sh "<plan-slug>"
@@ -174,6 +182,7 @@ bash scripts/codex-agent.sh "task" "agent-name"
 bash scripts/agent-branch-start.sh "task" "agent-name"
 python3 scripts/agent-file-locks.py claim --branch "$(git rev-parse --abbrev-ref HEAD)" <file...>
 bash scripts/agent-branch-finish.sh --branch "$(git rev-parse --abbrev-ref HEAD)"
+gx cleanup --branch "$(git rev-parse --abbrev-ref HEAD)"
 bash scripts/openspec/init-plan-workspace.sh "<plan-slug>"
 gx protect add release staging
 gx sync --check
@@ -290,6 +299,8 @@ NOTES
   - ${TOOL_NAME} setup asks for Y/N approval before global installs
   - In initialized repos, setup/install/fix block in-place writes on protected main by default
   - doctor auto-starts a sandbox agent branch/worktree when run on protected main
+  - agent-branch-finish merges by default and keeps agent branches/worktrees until explicit cleanup
+  - use '${SHORT_TOOL_NAME} cleanup' to remove merged agent branches/worktrees (optionally remote refs too)
   - Legacy command aliases are still supported: ${LEGACY_NAMES.join(', ')}`);
 
   if (outsideGitRepo) {
@@ -506,7 +517,7 @@ function ensurePackageScripts(repoRoot, dryRun) {
     'agent:codex': 'bash ./scripts/codex-agent.sh',
     'agent:branch:start': 'bash ./scripts/agent-branch-start.sh',
     'agent:branch:finish': 'bash ./scripts/agent-branch-finish.sh',
-    'agent:cleanup': 'bash ./scripts/agent-worktree-prune.sh',
+    'agent:cleanup': `${SHORT_TOOL_NAME} cleanup`,
     'agent:hooks:install': 'bash ./scripts/install-agent-git-hooks.sh',
     'agent:locks:claim': 'python3 ./scripts/agent-file-locks.py claim',
     'agent:locks:allow-delete': 'python3 ./scripts/agent-file-locks.py allow-delete',
@@ -1256,6 +1267,63 @@ function parseSyncArgs(rawArgs) {
   return options;
 }
 
+function parseCleanupArgs(rawArgs) {
+  const options = {
+    target: process.cwd(),
+    base: '',
+    branch: '',
+    dryRun: false,
+    forceDirty: false,
+    keepRemote: false,
+  };
+
+  for (let index = 0; index < rawArgs.length; index += 1) {
+    const arg = rawArgs[index];
+    if (arg === '--target') {
+      const next = rawArgs[index + 1];
+      if (!next) {
+        throw new Error('--target requires a path value');
+      }
+      options.target = next;
+      index += 1;
+      continue;
+    }
+    if (arg === '--base') {
+      const next = rawArgs[index + 1];
+      if (!next) {
+        throw new Error('--base requires a branch value');
+      }
+      options.base = next;
+      index += 1;
+      continue;
+    }
+    if (arg === '--branch') {
+      const next = rawArgs[index + 1];
+      if (!next) {
+        throw new Error('--branch requires an agent branch value');
+      }
+      options.branch = next;
+      index += 1;
+      continue;
+    }
+    if (arg === '--dry-run') {
+      options.dryRun = true;
+      continue;
+    }
+    if (arg === '--force-dirty') {
+      options.forceDirty = true;
+      continue;
+    }
+    if (arg === '--keep-remote') {
+      options.keepRemote = true;
+      continue;
+    }
+    throw new Error(`Unknown option: ${arg}`);
+  }
+
+  return options;
+}
+
 function syncOperation(repoRoot, strategy, baseRef, ffOnly) {
   if (strategy === 'rebase') {
     if (ffOnly) {
@@ -2284,6 +2352,39 @@ function copyCommands() {
   process.exitCode = 0;
 }
 
+function cleanup(rawArgs) {
+  const options = parseCleanupArgs(rawArgs);
+  const repoRoot = resolveRepoRoot(options.target);
+  const pruneScript = path.join(repoRoot, 'scripts', 'agent-worktree-prune.sh');
+  if (!fs.existsSync(pruneScript)) {
+    throw new Error(`Missing cleanup script: ${pruneScript}. Run '${SHORT_TOOL_NAME} setup' first.`);
+  }
+
+  const args = [pruneScript];
+  if (options.base) {
+    args.push('--base', options.base);
+  }
+  if (options.branch) {
+    args.push('--branch', options.branch);
+  }
+  if (options.forceDirty) {
+    args.push('--force-dirty');
+  }
+  if (options.dryRun) {
+    args.push('--dry-run');
+  }
+  args.push('--delete-branches');
+  if (!options.keepRemote) {
+    args.push('--delete-remote-branches');
+  }
+
+  const runResult = run('bash', args, { cwd: repoRoot, stdio: 'inherit' });
+  if (runResult.status !== 0) {
+    throw new Error('Cleanup command failed');
+  }
+  process.exitCode = 0;
+}
+
 function sync(rawArgs) {
   const options = parseSyncArgs(rawArgs);
   const repoRoot = resolveRepoRoot(options.target);
@@ -2632,6 +2733,11 @@ function main() {
     return;
   }
 
+  if (command === 'cleanup') {
+    cleanup(rest);
+    return;
+  }
+
   if (command === 'release') {
     release(rest);
     return;
diff --git a/scripts/agent-branch-finish.sh b/scripts/agent-branch-finish.sh
index a87cec4..17aa2f2 100755
--- a/scripts/agent-branch-finish.sh
+++ b/scripts/agent-branch-finish.sh
@@ -5,9 +5,26 @@ BASE_BRANCH=""
 BASE_BRANCH_EXPLICIT=0
 SOURCE_BRANCH=""
 PUSH_ENABLED=1
-DELETE_REMOTE_BRANCH=1
+DELETE_REMOTE_BRANCH=0
+DELETE_REMOTE_BRANCH_EXPLICIT=0
 MERGE_MODE="auto"
 GH_BIN="${MUSAFETY_GH_BIN:-gh}"
+CLEANUP_AFTER_MERGE_RAW="${MUSAFETY_FINISH_CLEANUP:-false}"
+
+normalize_bool() {
+  local raw="${1:-}"
+  local fallback="${2:-0}"
+  local lowered
+  lowered="$(printf '%s' "$raw" | tr '[:upper:]' '[:lower:]')"
+  case "$lowered" in
+    1|true|yes|on) printf '1' ;;
+    0|false|no|off) printf '0' ;;
+    '') printf '%s' "$fallback" ;;
+    *) printf '%s' "$fallback" ;;
+  esac
+}
+
+CLEANUP_AFTER_MERGE="$(normalize_bool "$CLEANUP_AFTER_MERGE_RAW" "0")"
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
@@ -26,6 +43,20 @@ while [[ $# -gt 0 ]]; do
       ;;
     --keep-remote-branch)
       DELETE_REMOTE_BRANCH=0
+      DELETE_REMOTE_BRANCH_EXPLICIT=1
+      shift
+      ;;
+    --delete-remote-branch)
+      DELETE_REMOTE_BRANCH=1
+      DELETE_REMOTE_BRANCH_EXPLICIT=1
+      shift
+      ;;
+    --cleanup)
+      CLEANUP_AFTER_MERGE=1
+      shift
+      ;;
+    --no-cleanup)
+      CLEANUP_AFTER_MERGE=0
       shift
       ;;
     --mode)
@@ -42,12 +73,16 @@ while [[ $# -gt 0 ]]; do
       ;;
     *)
       echo "[agent-branch-finish] Unknown argument: $1" >&2
-      echo "Usage: $0 [--base <branch>] [--branch <branch>] [--no-push] [--keep-remote-branch] [--mode auto|direct|pr|--via-pr|--direct-only]" >&2
+      echo "Usage: $0 [--base <branch>] [--branch <branch>] [--no-push] [--cleanup|--no-cleanup] [--keep-remote-branch|--delete-remote-branch] [--mode auto|direct|pr|--via-pr|--direct-only]" >&2
       exit 1
       ;;
   esac
 done
 
+if [[ "$CLEANUP_AFTER_MERGE" -eq 1 && "$DELETE_REMOTE_BRANCH_EXPLICIT" -eq 0 ]]; then
+  DELETE_REMOTE_BRANCH=1
+fi
+
 case "$MERGE_MODE" in
   auto|direct|pr) ;;
   *)
@@ -347,43 +382,58 @@ if [[ -x "${repo_root}/scripts/agent-file-locks.py" ]]; then
   python3 "${repo_root}/scripts/agent-file-locks.py" release --branch "$SOURCE_BRANCH" >/dev/null 2>&1 || true
 fi
 
-if [[ "$source_worktree" == "$repo_root" ]]; then
-  if is_clean_worktree "$source_worktree"; then
-    git -C "$source_worktree" checkout "$BASE_BRANCH" >/dev/null 2>&1 || true
-    if [[ "$PUSH_ENABLED" -eq 1 ]] && git -C "$repo_root" show-ref --verify --quiet "refs/remotes/origin/${BASE_BRANCH}"; then
-      git -C "$source_worktree" pull --ff-only origin "$BASE_BRANCH" >/dev/null 2>&1 || true
+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 "$BASE_BRANCH" >/dev/null 2>&1 || true
+fi
+
+if [[ "$CLEANUP_AFTER_MERGE" -eq 1 ]]; then
+  if [[ "$source_worktree" == "$repo_root" ]]; then
+    if is_clean_worktree "$source_worktree"; then
+      git -C "$source_worktree" checkout "$BASE_BRANCH" >/dev/null 2>&1 || true
+      if [[ "$PUSH_ENABLED" -eq 1 ]] && git -C "$repo_root" show-ref --verify --quiet "refs/remotes/origin/${BASE_BRANCH}"; then
+        git -C "$source_worktree" pull --ff-only origin "$BASE_BRANCH" >/dev/null 2>&1 || true
+      fi
     fi
+  elif [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
+    git -C "$source_worktree" checkout --detach >/dev/null 2>&1 || true
   fi
-elif [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
-  git -C "$source_worktree" checkout --detach >/dev/null 2>&1 || true
-fi
 
-if [[ "$source_worktree" != "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
-  git -C "$repo_root" worktree remove "$source_worktree" --force >/dev/null 2>&1 || true
-fi
+  if [[ "$source_worktree" != "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
+    git -C "$repo_root" worktree remove "$source_worktree" --force >/dev/null 2>&1 || true
+  fi
 
-git -C "$repo_root" branch -d "$SOURCE_BRANCH"
+  git -C "$repo_root" branch -d "$SOURCE_BRANCH"
 
-if [[ "$PUSH_ENABLED" -eq 1 && "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
-  if git -C "$repo_root" ls-remote --exit-code --heads origin "$SOURCE_BRANCH" >/dev/null 2>&1; then
-    git -C "$repo_root" push origin --delete "$SOURCE_BRANCH"
+  if [[ "$PUSH_ENABLED" -eq 1 && "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+    if git -C "$repo_root" ls-remote --exit-code --heads origin "$SOURCE_BRANCH" >/dev/null 2>&1; then
+      git -C "$repo_root" push origin --delete "$SOURCE_BRANCH"
+    fi
   fi
-fi
 
-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 "$BASE_BRANCH" >/dev/null 2>&1 || true
-fi
+  if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
+    prune_args=(--base "$BASE_BRANCH" --delete-branches)
+    if [[ "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+      prune_args+=(--delete-remote-branches)
+    fi
+    if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" "${prune_args[@]}"; then
+      echo "[agent-branch-finish] Warning: automatic worktree prune failed." >&2
+      echo "[agent-branch-finish] You can run manual cleanup: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH} --delete-branches" >&2
+    fi
+  fi
 
-if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
-  if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" --base "$BASE_BRANCH"; then
-    echo "[agent-branch-finish] Warning: automatic worktree prune failed." >&2
-    echo "[agent-branch-finish] You can run manual cleanup: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH}" >&2
+  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/worktree."
+  if [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
+    echo "[agent-branch-finish] Current worktree '${source_worktree}' still exists because it is the active shell cwd." >&2
+    echo "[agent-branch-finish] Leave this directory, then run: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH} --delete-branches" >&2
+  fi
+else
+  if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
+    if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" --base "$BASE_BRANCH"; then
+      echo "[agent-branch-finish] Warning: temporary worktree prune failed." >&2
+    fi
   fi
-fi
 
-echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and removed branch."
-if [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
-  echo "[agent-branch-finish] Current worktree '${source_worktree}' still exists because it is the active shell cwd." >&2
-  echo "[agent-branch-finish] Leave this directory, then run: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH}" >&2
+  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and kept source branch/worktree."
+  echo "[agent-branch-finish] Cleanup later with: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH} --delete-branches --delete-remote-branches"
 fi
diff --git a/scripts/agent-worktree-prune.sh b/scripts/agent-worktree-prune.sh
index ced73bc..7a08c28 100755
--- a/scripts/agent-worktree-prune.sh
+++ b/scripts/agent-worktree-prune.sh
@@ -5,6 +5,9 @@ BASE_BRANCH="${MUSAFETY_BASE_BRANCH:-}"
 BASE_BRANCH_EXPLICIT=0
 DRY_RUN=0
 FORCE_DIRTY=0
+DELETE_BRANCHES=0
+DELETE_REMOTE_BRANCHES=0
+TARGET_BRANCH=""
 
 if [[ -n "$BASE_BRANCH" ]]; then
   BASE_BRANCH_EXPLICIT=1
@@ -25,9 +28,21 @@ while [[ $# -gt 0 ]]; do
       FORCE_DIRTY=1
       shift
       ;;
+    --delete-branches)
+      DELETE_BRANCHES=1
+      shift
+      ;;
+    --delete-remote-branches)
+      DELETE_REMOTE_BRANCHES=1
+      shift
+      ;;
+    --branch)
+      TARGET_BRANCH="${2:-}"
+      shift 2
+      ;;
     *)
       echo "[agent-worktree-prune] Unknown argument: $1" >&2
-      echo "Usage: $0 [--base <branch>] [--dry-run] [--force-dirty]" >&2
+      echo "Usage: $0 [--base <branch>] [--dry-run] [--force-dirty] [--delete-branches] [--delete-remote-branches] [--branch <agent/...>]" >&2
       exit 1
       ;;
   esac
@@ -73,6 +88,11 @@ if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 && -z "$BASE_BRANCH" ]]; then
   exit 1
 fi
 
+if [[ -n "$TARGET_BRANCH" && "$TARGET_BRANCH" != agent/* ]]; then
+  echo "[agent-worktree-prune] --branch must reference an agent/* branch: ${TARGET_BRANCH}" >&2
+  exit 1
+fi
+
 if [[ "$BASE_BRANCH_EXPLICIT" -eq 0 ]]; then
   BASE_BRANCH="$(resolve_base_branch)"
 fi
@@ -124,6 +144,10 @@ process_entry() {
     branch="${branch_ref#refs/heads/}"
   fi
 
+  if [[ -n "$TARGET_BRANCH" && "$branch" != "$TARGET_BRANCH" ]]; then
+    return
+  fi
+
   if [[ "$wt" == "$current_pwd" ]]; then
     skipped_active=$((skipped_active + 1))
     echo "[agent-worktree-prune] Skipping active cwd worktree: ${wt}"
@@ -138,7 +162,9 @@ process_entry() {
     remove_reason="missing-branch"
   elif [[ "$branch" == agent/* ]]; then
     if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
-      remove_reason="merged-agent-branch"
+      if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
+        remove_reason="merged-agent-branch"
+      fi
     fi
   elif [[ "$branch" == __agent_integrate_* || "$branch" == __source-probe-* ]]; then
     remove_reason="temporary-worktree"
@@ -163,10 +189,16 @@ process_entry() {
   fi
 
   if git -C "$repo_root" show-ref --verify --quiet "refs/heads/${branch}" && ! branch_has_worktree "$branch"; then
-    if [[ "$branch" == agent/* ]]; then
+    if [[ "$branch" == agent/* && "$DELETE_BRANCHES" -eq 1 ]]; then
       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 merged branch: ${branch}"
+        if [[ "$DELETE_REMOTE_BRANCHES" -eq 1 ]]; then
+          if git -C "$repo_root" ls-remote --exit-code --heads origin "$branch" >/dev/null 2>&1; then
+            run_cmd git -C "$repo_root" push origin --delete "$branch" >/dev/null 2>&1 || true
+            echo "[agent-worktree-prune] Deleted merged remote branch: ${branch}"
+          fi
+        fi
       fi
     elif [[ "$branch" == __agent_integrate_* || "$branch" == __source-probe-* ]]; then
       run_cmd git -C "$repo_root" branch -D "$branch" >/dev/null 2>&1 || true
@@ -199,18 +231,29 @@ done < <(git -C "$repo_root" worktree list --porcelain)
 
 process_entry "$current_wt" "$current_branch_ref"
 
-while IFS= read -r branch; do
-  [[ -z "$branch" ]] && continue
-  if branch_has_worktree "$branch"; then
-    continue
-  fi
-  if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
-    if run_cmd git -C "$repo_root" branch -d "$branch" >/dev/null 2>&1; then
-      removed_branches=$((removed_branches + 1))
-      echo "[agent-worktree-prune] Deleted stale merged branch: ${branch}"
+if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
+  while IFS= read -r branch; do
+    [[ -z "$branch" ]] && continue
+    if [[ -n "$TARGET_BRANCH" && "$branch" != "$TARGET_BRANCH" ]]; then
+      continue
     fi
-  fi
-done < <(git -C "$repo_root" for-each-ref --format='%(refname:short)' refs/heads/agent)
+    if branch_has_worktree "$branch"; then
+      continue
+    fi
+    if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
+      if run_cmd git -C "$repo_root" branch -d "$branch" >/dev/null 2>&1; then
+        removed_branches=$((removed_branches + 1))
+        echo "[agent-worktree-prune] Deleted stale merged branch: ${branch}"
+        if [[ "$DELETE_REMOTE_BRANCHES" -eq 1 ]]; then
+          if git -C "$repo_root" ls-remote --exit-code --heads origin "$branch" >/dev/null 2>&1; then
+            run_cmd git -C "$repo_root" push origin --delete "$branch" >/dev/null 2>&1 || true
+            echo "[agent-worktree-prune] Deleted stale merged remote branch: ${branch}"
+          fi
+        fi
+      fi
+    fi
+  done < <(git -C "$repo_root" for-each-ref --format='%(refname:short)' refs/heads/agent)
+fi
 
 run_cmd git -C "$repo_root" worktree prune
 
diff --git a/templates/AGENTS.multiagent-safety.md b/templates/AGENTS.multiagent-safety.md
index a883a72..7e79035 100644
--- a/templates/AGENTS.multiagent-safety.md
+++ b/templates/AGENTS.multiagent-safety.md
@@ -11,7 +11,9 @@
 - If ownership is unclear or overlaps, stop that edit, post a blocker comment, and let the leader/integrator reassign scope.
 - For git isolation, each agent must start on a dedicated branch via `scripts/agent-branch-start.sh "<task-or-plan>" "<agent-name>"`.
 - Treat the base branch (`main` or the user's current local base branch) as read-only while the agent branch is active.
-- Agent completion defaults to `scripts/codex-agent.sh`, which now auto-finishes the branch (auto-commit changed files, push/create PR, attempt merge, clean branch/worktree, and pull the local base branch after merge).
+- Agent completion defaults to `scripts/codex-agent.sh`, which auto-finishes the branch (auto-commit changed files, push/create PR, attempt merge, and pull the local base branch after merge).
+- Auto-finish keeps the sandbox branch/worktree by default so conflict follow-ups and audits stay reproducible.
+- Use explicit cleanup when done: `gx cleanup --branch "<agent-branch>"` (or `gx cleanup` for all merged agent branches).
 - If codex-agent auto-finish cannot complete, immediately run `scripts/agent-branch-finish.sh --branch "<agent-branch>" --via-pr` and keep the branch open until checks/review pass.
 - If merge/rebase conflicts block auto-finish, run a conflict-resolution review pass in that sandbox branch, then rerun `agent-branch-finish.sh --via-pr` until merged.
 - Per-message loop is mandatory: for every new user message/task, start a fresh agent branch/worktree, claim ownership locks, implement and verify, finish via PR/merge cleanup, then repeat for the next message/task.
diff --git a/templates/codex/skills/guardex/SKILL.md b/templates/codex/skills/guardex/SKILL.md
index fbd3ab6..4d9f32f 100644
--- a/templates/codex/skills/guardex/SKILL.md
+++ b/templates/codex/skills/guardex/SKILL.md
@@ -36,4 +36,6 @@ gx scan
 - Keep agent work isolated (`agent/*` branches + lock claims).
 - For every new user message/task, restart the full loop on a fresh agent branch/worktree.
 - For one-command Codex sandbox startup, use `bash scripts/codex-agent.sh "<task>" "<agent-name>"`.
+- `scripts/codex-agent.sh` auto-syncs the sandbox branch against base before each task and auto-finishes merge/PR flow after Codex exits.
+- Auto-finish keeps the branch/worktree by default; remove merged branches explicitly with `gx cleanup` (or `gx cleanup --branch "<agent-branch>"`).
 - Do not bypass protected branch safeguards unless explicitly required.
diff --git a/templates/scripts/agent-branch-finish.sh b/templates/scripts/agent-branch-finish.sh
index a87cec4..17aa2f2 100755
--- a/templates/scripts/agent-branch-finish.sh
+++ b/templates/scripts/agent-branch-finish.sh
@@ -5,9 +5,26 @@ BASE_BRANCH=""
 BASE_BRANCH_EXPLICIT=0
 SOURCE_BRANCH=""
 PUSH_ENABLED=1
-DELETE_REMOTE_BRANCH=1
+DELETE_REMOTE_BRANCH=0
+DELETE_REMOTE_BRANCH_EXPLICIT=0
 MERGE_MODE="auto"
 GH_BIN="${MUSAFETY_GH_BIN:-gh}"
+CLEANUP_AFTER_MERGE_RAW="${MUSAFETY_FINISH_CLEANUP:-false}"
+
+normalize_bool() {
+  local raw="${1:-}"
+  local fallback="${2:-0}"
+  local lowered
+  lowered="$(printf '%s' "$raw" | tr '[:upper:]' '[:lower:]')"
+  case "$lowered" in
+    1|true|yes|on) printf '1' ;;
+    0|false|no|off) printf '0' ;;
+    '') printf '%s' "$fallback" ;;
+    *) printf '%s' "$fallback" ;;
+  esac
+}
+
+CLEANUP_AFTER_MERGE="$(normalize_bool "$CLEANUP_AFTER_MERGE_RAW" "0")"
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
@@ -26,6 +43,20 @@ while [[ $# -gt 0 ]]; do
       ;;
     --keep-remote-branch)
       DELETE_REMOTE_BRANCH=0
+      DELETE_REMOTE_BRANCH_EXPLICIT=1
+      shift
+      ;;
+    --delete-remote-branch)
+      DELETE_REMOTE_BRANCH=1
+      DELETE_REMOTE_BRANCH_EXPLICIT=1
+      shift
+      ;;
+    --cleanup)
+      CLEANUP_AFTER_MERGE=1
+      shift
+      ;;
+    --no-cleanup)
+      CLEANUP_AFTER_MERGE=0
       shift
       ;;
     --mode)
@@ -42,12 +73,16 @@ while [[ $# -gt 0 ]]; do
       ;;
     *)
       echo "[agent-branch-finish] Unknown argument: $1" >&2
-      echo "Usage: $0 [--base <branch>] [--branch <branch>] [--no-push] [--keep-remote-branch] [--mode auto|direct|pr|--via-pr|--direct-only]" >&2
+      echo "Usage: $0 [--base <branch>] [--branch <branch>] [--no-push] [--cleanup|--no-cleanup] [--keep-remote-branch|--delete-remote-branch] [--mode auto|direct|pr|--via-pr|--direct-only]" >&2
       exit 1
       ;;
   esac
 done
 
+if [[ "$CLEANUP_AFTER_MERGE" -eq 1 && "$DELETE_REMOTE_BRANCH_EXPLICIT" -eq 0 ]]; then
+  DELETE_REMOTE_BRANCH=1
+fi
+
 case "$MERGE_MODE" in
   auto|direct|pr) ;;
   *)
@@ -347,43 +382,58 @@ if [[ -x "${repo_root}/scripts/agent-file-locks.py" ]]; then
   python3 "${repo_root}/scripts/agent-file-locks.py" release --branch "$SOURCE_BRANCH" >/dev/null 2>&1 || true
 fi
 
-if [[ "$source_worktree" == "$repo_root" ]]; then
-  if is_clean_worktree "$source_worktree"; then
-    git -C "$source_worktree" checkout "$BASE_BRANCH" >/dev/null 2>&1 || true
-    if [[ "$PUSH_ENABLED" -eq 1 ]] && git -C "$repo_root" show-ref --verify --quiet "refs/remotes/origin/${BASE_BRANCH}"; then
-      git -C "$source_worktree" pull --ff-only origin "$BASE_BRANCH" >/dev/null 2>&1 || true
+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 "$BASE_BRANCH" >/dev/null 2>&1 || true
+fi
+
+if [[ "$CLEANUP_AFTER_MERGE" -eq 1 ]]; then
+  if [[ "$source_worktree" == "$repo_root" ]]; then
+    if is_clean_worktree "$source_worktree"; then
+      git -C "$source_worktree" checkout "$BASE_BRANCH" >/dev/null 2>&1 || true
+      if [[ "$PUSH_ENABLED" -eq 1 ]] && git -C "$repo_root" show-ref --verify --quiet "refs/remotes/origin/${BASE_BRANCH}"; then
+        git -C "$source_worktree" pull --ff-only origin "$BASE_BRANCH" >/dev/null 2>&1 || true
+      fi
     fi
+  elif [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
+    git -C "$source_worktree" checkout --detach >/dev/null 2>&1 || true
   fi
-elif [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
-  git -C "$source_worktree" checkout --detach >/dev/null 2>&1 || true
-fi
 
-if [[ "$source_worktree" != "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
-  git -C "$repo_root" worktree remove "$source_worktree" --force >/dev/null 2>&1 || true
-fi
+  if [[ "$source_worktree" != "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
+    git -C "$repo_root" worktree remove "$source_worktree" --force >/dev/null 2>&1 || true
+  fi
 
-git -C "$repo_root" branch -d "$SOURCE_BRANCH"
+  git -C "$repo_root" branch -d "$SOURCE_BRANCH"
 
-if [[ "$PUSH_ENABLED" -eq 1 && "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
-  if git -C "$repo_root" ls-remote --exit-code --heads origin "$SOURCE_BRANCH" >/dev/null 2>&1; then
-    git -C "$repo_root" push origin --delete "$SOURCE_BRANCH"
+  if [[ "$PUSH_ENABLED" -eq 1 && "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+    if git -C "$repo_root" ls-remote --exit-code --heads origin "$SOURCE_BRANCH" >/dev/null 2>&1; then
+      git -C "$repo_root" push origin --delete "$SOURCE_BRANCH"
+    fi
   fi
-fi
 
-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 "$BASE_BRANCH" >/dev/null 2>&1 || true
-fi
+  if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
+    prune_args=(--base "$BASE_BRANCH" --delete-branches)
+    if [[ "$DELETE_REMOTE_BRANCH" -eq 1 ]]; then
+      prune_args+=(--delete-remote-branches)
+    fi
+    if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" "${prune_args[@]}"; then
+      echo "[agent-branch-finish] Warning: automatic worktree prune failed." >&2
+      echo "[agent-branch-finish] You can run manual cleanup: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH} --delete-branches" >&2
+    fi
+  fi
 
-if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
-  if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" --base "$BASE_BRANCH"; then
-    echo "[agent-branch-finish] Warning: automatic worktree prune failed." >&2
-    echo "[agent-branch-finish] You can run manual cleanup: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH}" >&2
+  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and cleaned source branch/worktree."
+  if [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
+    echo "[agent-branch-finish] Current worktree '${source_worktree}' still exists because it is the active shell cwd." >&2
+    echo "[agent-branch-finish] Leave this directory, then run: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH} --delete-branches" >&2
+  fi
+else
+  if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
+    if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" --base "$BASE_BRANCH"; then
+      echo "[agent-branch-finish] Warning: temporary worktree prune failed." >&2
+    fi
   fi
-fi
 
-echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and removed branch."
-if [[ "$source_worktree" == "$current_worktree" && "$source_worktree" == "${repo_root}/.omx/agent-worktrees"/* ]]; then
-  echo "[agent-branch-finish] Current worktree '${source_worktree}' still exists because it is the active shell cwd." >&2
-  echo "[agent-branch-finish] Leave this directory, then run: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH}" >&2
+  echo "[agent-branch-finish] Merged '${SOURCE_BRANCH}' into '${BASE_BRANCH}' via ${merge_status} flow and kept source branch/worktree."
+  echo "[agent-branch-finish] Cleanup later with: bash scripts/agent-worktree-prune.sh --base ${BASE_BRANCH} --delete-branches --delete-remote-branches"
 fi
diff --git a/templates/scripts/agent-worktree-prune.sh b/templates/scripts/agent-worktree-prune.sh
index ced73bc..7a08c28 100644
--- a/templates/scripts/agent-worktree-prune.sh
+++ b/templates/scripts/agent-worktree-prune.sh
@@ -5,6 +5,9 @@ BASE_BRANCH="${MUSAFETY_BASE_BRANCH:-}"
 BASE_BRANCH_EXPLICIT=0
 DRY_RUN=0
 FORCE_DIRTY=0
+DELETE_BRANCHES=0
+DELETE_REMOTE_BRANCHES=0
+TARGET_BRANCH=""
 
 if [[ -n "$BASE_BRANCH" ]]; then
   BASE_BRANCH_EXPLICIT=1
@@ -25,9 +28,21 @@ while [[ $# -gt 0 ]]; do
       FORCE_DIRTY=1
       shift
       ;;
+    --delete-branches)
+      DELETE_BRANCHES=1
+      shift
+      ;;
+    --delete-remote-branches)
+      DELETE_REMOTE_BRANCHES=1
+      shift
+      ;;
+    --branch)
+      TARGET_BRANCH="${2:-}"
+      shift 2
+      ;;
     *)
       echo "[agent-worktree-prune] Unknown argument: $1" >&2
-      echo "Usage: $0 [--base <branch>] [--dry-run] [--force-dirty]" >&2
+      echo "Usage: $0 [--base <branch>] [--dry-run] [--force-dirty] [--delete-branches] [--delete-remote-branches] [--branch <agent/...>]" >&2
       exit 1
       ;;
   esac
@@ -73,6 +88,11 @@ if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 && -z "$BASE_BRANCH" ]]; then
   exit 1
 fi
 
+if [[ -n "$TARGET_BRANCH" && "$TARGET_BRANCH" != agent/* ]]; then
+  echo "[agent-worktree-prune] --branch must reference an agent/* branch: ${TARGET_BRANCH}" >&2
+  exit 1
+fi
+
 if [[ "$BASE_BRANCH_EXPLICIT" -eq 0 ]]; then
   BASE_BRANCH="$(resolve_base_branch)"
 fi
@@ -124,6 +144,10 @@ process_entry() {
     branch="${branch_ref#refs/heads/}"
   fi
 
+  if [[ -n "$TARGET_BRANCH" && "$branch" != "$TARGET_BRANCH" ]]; then
+    return
+  fi
+
   if [[ "$wt" == "$current_pwd" ]]; then
     skipped_active=$((skipped_active + 1))
     echo "[agent-worktree-prune] Skipping active cwd worktree: ${wt}"
@@ -138,7 +162,9 @@ process_entry() {
     remove_reason="missing-branch"
   elif [[ "$branch" == agent/* ]]; then
     if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
-      remove_reason="merged-agent-branch"
+      if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
+        remove_reason="merged-agent-branch"
+      fi
     fi
   elif [[ "$branch" == __agent_integrate_* || "$branch" == __source-probe-* ]]; then
     remove_reason="temporary-worktree"
@@ -163,10 +189,16 @@ process_entry() {
   fi
 
   if git -C "$repo_root" show-ref --verify --quiet "refs/heads/${branch}" && ! branch_has_worktree "$branch"; then
-    if [[ "$branch" == agent/* ]]; then
+    if [[ "$branch" == agent/* && "$DELETE_BRANCHES" -eq 1 ]]; then
       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 merged branch: ${branch}"
+        if [[ "$DELETE_REMOTE_BRANCHES" -eq 1 ]]; then
+          if git -C "$repo_root" ls-remote --exit-code --heads origin "$branch" >/dev/null 2>&1; then
+            run_cmd git -C "$repo_root" push origin --delete "$branch" >/dev/null 2>&1 || true
+            echo "[agent-worktree-prune] Deleted merged remote branch: ${branch}"
+          fi
+        fi
       fi
     elif [[ "$branch" == __agent_integrate_* || "$branch" == __source-probe-* ]]; then
       run_cmd git -C "$repo_root" branch -D "$branch" >/dev/null 2>&1 || true
@@ -199,18 +231,29 @@ done < <(git -C "$repo_root" worktree list --porcelain)
 
 process_entry "$current_wt" "$current_branch_ref"
 
-while IFS= read -r branch; do
-  [[ -z "$branch" ]] && continue
-  if branch_has_worktree "$branch"; then
-    continue
-  fi
-  if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
-    if run_cmd git -C "$repo_root" branch -d "$branch" >/dev/null 2>&1; then
-      removed_branches=$((removed_branches + 1))
-      echo "[agent-worktree-prune] Deleted stale merged branch: ${branch}"
+if [[ "$DELETE_BRANCHES" -eq 1 ]]; then
+  while IFS= read -r branch; do
+    [[ -z "$branch" ]] && continue
+    if [[ -n "$TARGET_BRANCH" && "$branch" != "$TARGET_BRANCH" ]]; then
+      continue
     fi
-  fi
-done < <(git -C "$repo_root" for-each-ref --format='%(refname:short)' refs/heads/agent)
+    if branch_has_worktree "$branch"; then
+      continue
+    fi
+    if git -C "$repo_root" merge-base --is-ancestor "$branch" "$BASE_BRANCH"; then
+      if run_cmd git -C "$repo_root" branch -d "$branch" >/dev/null 2>&1; then
+        removed_branches=$((removed_branches + 1))
+        echo "[agent-worktree-prune] Deleted stale merged branch: ${branch}"
+        if [[ "$DELETE_REMOTE_BRANCHES" -eq 1 ]]; then
+          if git -C "$repo_root" ls-remote --exit-code --heads origin "$branch" >/dev/null 2>&1; then
+            run_cmd git -C "$repo_root" push origin --delete "$branch" >/dev/null 2>&1 || true
+            echo "[agent-worktree-prune] Deleted stale merged remote branch: ${branch}"
+          fi
+        fi
+      fi
+    fi
+  done < <(git -C "$repo_root" for-each-ref --format='%(refname:short)' refs/heads/agent)
+fi
 
 run_cmd git -C "$repo_root" worktree prune
 
diff --git a/templates/scripts/codex-agent.sh b/templates/scripts/codex-agent.sh
index 09cacf5..136c59c 100755
--- a/templates/scripts/codex-agent.sh
+++ b/templates/scripts/codex-agent.sh
@@ -8,6 +8,7 @@ BASE_BRANCH_EXPLICIT=0
 CODEX_BIN="${MUSAFETY_CODEX_BIN:-codex}"
 AUTO_FINISH_RAW="${MUSAFETY_CODEX_AUTO_FINISH:-true}"
 AUTO_REVIEW_ON_CONFLICT_RAW="${MUSAFETY_CODEX_AUTO_REVIEW_ON_CONFLICT:-true}"
+AUTO_CLEANUP_RAW="${MUSAFETY_CODEX_AUTO_CLEANUP:-false}"
 
 normalize_bool() {
   local raw="${1:-}"
@@ -24,6 +25,7 @@ normalize_bool() {
 
 AUTO_FINISH="$(normalize_bool "$AUTO_FINISH_RAW" "1")"
 AUTO_REVIEW_ON_CONFLICT="$(normalize_bool "$AUTO_REVIEW_ON_CONFLICT_RAW" "1")"
+AUTO_CLEANUP="$(normalize_bool "$AUTO_CLEANUP_RAW" "0")"
 
 if [[ -n "$BASE_BRANCH" ]]; then
   BASE_BRANCH_EXPLICIT=1
@@ -64,6 +66,14 @@ while [[ $# -gt 0 ]]; do
       AUTO_REVIEW_ON_CONFLICT=0
       shift
       ;;
+    --cleanup)
+      AUTO_CLEANUP=1
+      shift
+      ;;
+    --no-cleanup)
+      AUTO_CLEANUP=0
+      shift
+      ;;
     --)
       shift
       break
@@ -133,6 +143,75 @@ has_origin_remote() {
   git -C "$repo_root" remote get-url origin >/dev/null 2>&1
 }
 
+resolve_worktree_base_branch() {
+  local wt="$1"
+  if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 && -n "$BASE_BRANCH" ]]; then
+    printf '%s' "$BASE_BRANCH"
+    return 0
+  fi
+
+  local branch
+  branch="$(git -C "$wt" rev-parse --abbrev-ref HEAD 2>/dev/null || true)"
+  if [[ -z "$branch" || "$branch" == "HEAD" ]]; then
+    return 0
+  fi
+
+  local stored_base
+  stored_base="$(git -C "$repo_root" config --get "branch.${branch}.musafetyBase" || true)"
+  if [[ -n "$stored_base" ]]; then
+    printf '%s' "$stored_base"
+    return 0
+  fi
+
+  local configured_base
+  configured_base="$(git -C "$repo_root" config --get multiagent.baseBranch || true)"
+  if [[ -n "$configured_base" ]]; then
+    printf '%s' "$configured_base"
+  fi
+}
+
+sync_worktree_with_base() {
+  local wt="$1"
+  if ! has_origin_remote; then
+    return 0
+  fi
+
+  local base_branch
+  base_branch="$(resolve_worktree_base_branch "$wt")"
+  if [[ -z "$base_branch" ]]; then
+    return 0
+  fi
+
+  if ! git -C "$wt" fetch origin "$base_branch" --quiet; then
+    echo "[codex-agent] Warning: could not fetch origin/${base_branch} before task start." >&2
+    return 0
+  fi
+
+  if ! git -C "$wt" show-ref --verify --quiet "refs/remotes/origin/${base_branch}"; then
+    return 0
+  fi
+
+  local behind_count
+  behind_count="$(git -C "$wt" rev-list --left-right --count "HEAD...origin/${base_branch}" 2>/dev/null | awk '{print $2}')"
+  behind_count="${behind_count:-0}"
+  if [[ "$behind_count" -le 0 ]]; then
+    return 0
+  fi
+
+  local branch
+  branch="$(git -C "$wt" rev-parse --abbrev-ref HEAD 2>/dev/null || true)"
+  echo "[codex-agent] Task sync: '${branch}' is behind origin/${base_branch} by ${behind_count} commit(s). Rebasing before launch..."
+  if ! git -C "$wt" rebase "origin/${base_branch}"; then
+    echo "[codex-agent] Task sync failed. Resolve and continue in sandbox:" >&2
+    echo "  git -C \"$wt\" rebase --continue" >&2
+    echo "  # or abort" >&2
+    echo "  git -C \"$wt\" rebase --abort" >&2
+    return 1
+  fi
+  echo "[codex-agent] Task sync complete."
+  return 0
+}
+
 worktree_has_changes() {
   local wt="$1"
   if ! git -C "$wt" diff --quiet -- . ":(exclude).omx/state/agent-file-locks.json"; then
@@ -224,6 +303,9 @@ run_finish_flow() {
   if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 ]]; then
     finish_args+=(--base "$BASE_BRANCH")
   fi
+  if [[ "$AUTO_CLEANUP" -eq 1 ]]; then
+    finish_args+=(--cleanup)
+  fi
 
   if has_origin_remote; then
     if command -v gh >/dev/null 2>&1 || command -v "${MUSAFETY_GH_BIN:-gh}" >/dev/null 2>&1; then
@@ -268,6 +350,10 @@ run_finish_flow() {
   return 1
 }
 
+if ! sync_worktree_with_base "$worktree_path"; then
+  exit 1
+fi
+
 echo "[codex-agent] Launching ${CODEX_BIN} in sandbox: $worktree_path"
 cd "$worktree_path"
 set +e
@@ -282,7 +368,11 @@ auto_finish_completed=0
 worktree_branch="$(git -C "$worktree_path" rev-parse --abbrev-ref HEAD 2>/dev/null || true)"
 
 if [[ "$AUTO_FINISH" -eq 1 && -n "$worktree_branch" && "$worktree_branch" != "HEAD" ]]; then
-  echo "[codex-agent] Auto-finish enabled: commit -> push/PR -> merge -> cleanup." 
+  if [[ "$AUTO_CLEANUP" -eq 1 ]]; then
+    echo "[codex-agent] Auto-finish enabled: commit -> push/PR -> merge -> cleanup."
+  else
+    echo "[codex-agent] Auto-finish enabled: commit -> push/PR -> merge (keep branch/worktree)."
+  fi
   if auto_commit_worktree_changes "$worktree_path" "$worktree_branch"; then
     if run_finish_flow "$worktree_path" "$worktree_branch"; then
       auto_finish_completed=1
@@ -311,6 +401,9 @@ if [[ -x "${repo_root}/scripts/agent-worktree-prune.sh" ]]; then
   if [[ "$BASE_BRANCH_EXPLICIT" -eq 1 ]]; then
     prune_args+=(--base "$BASE_BRANCH")
   fi
+  if [[ "$AUTO_CLEANUP" -eq 1 ]]; then
+    prune_args+=(--delete-branches --delete-remote-branches)
+  fi
   if ! bash "${repo_root}/scripts/agent-worktree-prune.sh" "${prune_args[@]}"; then
     echo "[codex-agent] Warning: automatic worktree cleanup failed." >&2
   fi
@@ -321,8 +414,13 @@ if [[ ! -d "$worktree_path" ]]; then
 else
   worktree_branch="$(git -C "$worktree_path" rev-parse --abbrev-ref HEAD 2>/dev/null || true)"
   echo "[codex-agent] Sandbox worktree kept: $worktree_path"
-  if [[ "$auto_finish_completed" -eq 0 && -n "$worktree_branch" && "$worktree_branch" != "HEAD" ]]; then
-    echo "[codex-agent] If finished, merge + clean with: bash scripts/agent-branch-finish.sh --branch \"${worktree_branch}\" --via-pr"
+  if [[ -n "$worktree_branch" && "$worktree_branch" != "HEAD" ]]; then
+    if [[ "$auto_finish_completed" -eq 1 ]]; then
+      echo "[codex-agent] Branch kept intentionally. Cleanup on demand: gx cleanup --branch \"${worktree_branch}\""
+    else
+      echo "[codex-agent] If finished, merge with: bash scripts/agent-branch-finish.sh --branch \"${worktree_branch}\" --via-pr"
+      echo "[codex-agent] Cleanup on demand: gx cleanup --branch \"${worktree_branch}\""
+    fi
   fi
 fi
 
diff --git a/test/install.test.js b/test/install.test.js
index 5ddb241..fe8c57f 100644
--- a/test/install.test.js
+++ b/test/install.test.js
@@ -216,7 +216,7 @@ test('setup provisions workflow files and repo config', () => {
   assert.equal(packageJson.scripts['agent:branch:sync'], 'gx sync');
   assert.equal(packageJson.scripts['agent:branch:sync:check'], 'gx sync --check');
   assert.equal(packageJson.scripts['agent:safety:setup'], 'gx setup');
-  assert.equal(packageJson.scripts['agent:cleanup'], 'bash ./scripts/agent-worktree-prune.sh');
+  assert.equal(packageJson.scripts['agent:cleanup'], 'gx cleanup');
 
   const agentsContent = fs.readFileSync(path.join(repoDir, 'AGENTS.md'), 'utf8');
   assert.equal(agentsContent.includes('<!-- multiagent-safety:START -->'), true);
@@ -554,7 +554,7 @@ test('agent-branch-finish infers base from source branch metadata and updates ma
   );
 
   const localBranchExists = runCmd('git', ['show-ref', '--verify', '--quiet', `refs/heads/${agentBranch}`], repoDir);
-  assert.equal(localBranchExists.status, 1, localBranchExists.stderr || localBranchExists.stdout);
+  assert.equal(localBranchExists.status, 0, localBranchExists.stderr || localBranchExists.stdout);
 });
 
 test('default invocation runs non-mutating status output', () => {
@@ -743,7 +743,7 @@ test('pre-commit blocks protected branch commits even from VS Code Source Contro
   assert.match(hookResult.stderr, /Direct commits on protected branches are blocked/);
 });
 
-test('codex-agent launches codex inside a fresh sandbox worktree and auto-prunes clean branches on exit', () => {
+test('codex-agent launches codex inside a fresh sandbox worktree and keeps branch/worktree by default', () => {
   const repoDir = initRepo();
   seedCommit(repoDir);
 
@@ -782,7 +782,7 @@ test('codex-agent launches codex inside a fresh sandbox worktree and auto-prunes
   assert.equal(launch.status, 0, launch.stderr || launch.stdout);
   assert.match(launch.stdout, /\[codex-agent\] Launching codex in sandbox:/);
   assert.match(launch.stdout, /\[codex-agent\] Session ended \(exit=0\)\. Running worktree cleanup\.\.\./);
-  assert.match(launch.stdout, /\[codex-agent\] Auto-cleaned sandbox worktree:/);
+  assert.match(launch.stdout, /\[codex-agent\] Sandbox worktree kept:/);
 
   const launchedCwd = fs.readFileSync(cwdMarker, 'utf8').trim();
   assert.match(
@@ -793,10 +793,10 @@ test('codex-agent launches codex inside a fresh sandbox worktree and auto-prunes
   const launchedArgs = fs.readFileSync(argsMarker, 'utf8').trim();
   assert.match(launchedArgs, /--model gpt-5\.4-mini/);
 
-  assert.equal(fs.existsSync(launchedCwd), false, 'clean codex-agent sandbox should auto-prune on exit');
+  assert.equal(fs.existsSync(launchedCwd), true, 'clean codex-agent sandbox should stay available by default');
   const launchedBranch = extractCreatedBranch(launch.stdout);
   const branchResult = runCmd('git', ['show-ref', '--verify', '--quiet', `refs/heads/${launchedBranch}`], repoDir);
-  assert.notEqual(branchResult.status, 0, 'clean auto-pruned branch should be removed locally');
+  assert.equal(branchResult.status, 0, 'agent branch should remain after default codex-agent run');
 });
 
 test('codex-agent supports --codex-bin override before positional arguments', () => {
@@ -845,7 +845,7 @@ test('codex-agent supports --codex-bin override before positional arguments', ()
   );
   assert.equal(launch.status, 0, launch.stderr || launch.stdout);
   assert.match(launch.stdout, /\[codex-agent\] Launching .* in sandbox:/);
-  assert.match(launch.stdout, /\[codex-agent\] Auto-cleaned sandbox worktree:/);
+  assert.match(launch.stdout, /\[codex-agent\] Sandbox worktree kept:/);
 
   const launchedCwd = fs.readFileSync(cwdMarker, 'utf8').trim();
   assert.match(
@@ -854,7 +854,7 @@ test('codex-agent supports --codex-bin override before positional arguments', ()
   );
   const launchedArgs = fs.readFileSync(argsMarker, 'utf8').trim();
   assert.match(launchedArgs, /--model gpt-5\.4-mini/);
-  assert.equal(fs.existsSync(launchedCwd), false, 'override invocation should still auto-prune clean sandbox');
+  assert.equal(fs.existsSync(launchedCwd), true, 'override invocation should keep sandbox unless cleanup is requested');
 });
 
 test('codex-agent keeps dirty sandbox worktrees after session exit', () => {
@@ -961,17 +961,17 @@ exit 1
     },
   );
   assert.equal(launch.status, 0, launch.stderr || launch.stdout);
-  assert.match(launch.stdout, /\[codex-agent\] Auto-finish enabled: commit -> push\/PR -> merge -> cleanup\./);
+  assert.match(launch.stdout, /\[codex-agent\] Auto-finish enabled: commit -> push\/PR -> merge \(keep branch\/worktree\)\./);
   assert.match(launch.stdout, /\[codex-agent\] Auto-finish completed for/);
-  assert.match(launch.stdout, /\[codex-agent\] Auto-cleaned sandbox worktree:/);
+  assert.match(launch.stdout, /\[codex-agent\] Sandbox worktree kept:/);
 
   const launchedCwd = fs.readFileSync(cwdMarker, 'utf8').trim();
-  assert.equal(fs.existsSync(launchedCwd), false, 'auto-finished sandbox should be removed');
+  assert.equal(fs.existsSync(launchedCwd), true, 'auto-finished sandbox should stay until explicit cleanup');
   const launchedBranch = extractCreatedBranch(launch.stdout);
   result = runCmd('git', ['show-ref', '--verify', '--quiet', `refs/heads/${launchedBranch}`], repoDir);
-  assert.notEqual(result.status, 0, 'auto-finished branch should be removed locally');
+  assert.equal(result.status, 0, 'auto-finished branch should remain locally by default');
   result = runCmd('git', ['ls-remote', '--heads', 'origin', launchedBranch], repoDir);
-  assert.equal(result.stdout.trim(), '', 'auto-finished branch should be removed on origin');
+  assert.match(result.stdout, /refs\/heads\//, 'auto-finished branch should remain on origin by default');
 
   const launchedArgs = fs.readFileSync(argsMarker, 'utf8').trim();
   assert.match(launchedArgs, /--model gpt-5\.4-mini/);
@@ -1157,11 +1157,11 @@ test('agent-branch-finish auto-syncs source branch when behind origin/dev', () =
   assert.match(finish.stderr, /Auto-sync complete \(behind now: 0\)/);
   assert.match(
     finish.stdout,
-    /Merged 'agent\/test-finish-sync-guard' into 'dev' via direct flow and removed branch\./,
+    /Merged 'agent\/test-finish-sync-guard' into 'dev' via direct flow and kept source branch\/worktree\./,
   );
 
   result = runCmd('git', ['show-ref', '--verify', '--quiet', 'refs/heads/agent/test-finish-sync-guard'], repoDir);
-  assert.notEqual(result.status, 0, 'agent branch should be deleted locally after finish');
+  assert.equal(result.status, 0, 'agent branch should stay locally after finish by default');
 });
 
 test('agent-branch-finish pr mode continues cleanup when gh merge only fails local branch deletion', () => {
@@ -1207,7 +1207,7 @@ exit 1
 
   const finish = runCmd(
     'bash',
-    ['scripts/agent-branch-finish.sh', '--branch', 'agent/test-pr-delete-error', '--mode', 'pr'],
+    ['scripts/agent-branch-finish.sh', '--branch', 'agent/test-pr-delete-error', '--mode', 'pr', '--cleanup'],
     repoDir,
     { MUSAFETY_GH_BIN: fakeGhPath },
   );
@@ -1218,7 +1218,7 @@ exit 1
   );
   assert.match(
     finish.stdout,
-    /Merged 'agent\/test-pr-delete-error' into 'dev' via pr flow and removed branch\./,
+    /Merged 'agent\/test-pr-delete-error' into 'dev' via pr flow and cleaned source branch\/worktree\./,
   );
 
   result = runCmd('git', ['show-ref', '--verify', '--quiet', 'refs/heads/agent/test-pr-delete-error'], repoDir);
@@ -1527,7 +1527,7 @@ exit 1
   assert.equal(args, 'i -g @fission-ai/openspec @imdeadpool/codex-account-switcher');
 });
 
-test('worktree prune removes merged agent worktrees and branches', () => {
+test('worktree prune keeps merged agent worktrees/branches unless delete flags are set', () => {
   const repoDir = initRepo();
   let result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
@@ -1540,10 +1540,15 @@ test('worktree prune removes merged agent worktrees and branches', () => {
 
   result = runCmd('bash', ['scripts/agent-worktree-prune.sh'], repoDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
-  assert.equal(fs.existsSync(worktreePath), false);
 
   const branchResult = runCmd('git', ['show-ref', '--verify', '--quiet', 'refs/heads/agent/test-prune'], repoDir);
-  assert.notEqual(branchResult.status, 0, 'merged agent branch should be removed by prune');
+  assert.equal(branchResult.status, 0, 'merged agent branch should remain by default');
+
+  result = runCmd('bash', ['scripts/agent-worktree-prune.sh', '--delete-branches'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  assert.equal(fs.existsSync(worktreePath), false);
+  const branchAfterDelete = runCmd('git', ['show-ref', '--verify', '--quiet', 'refs/heads/agent/test-prune'], repoDir);
+  assert.notEqual(branchAfterDelete.status, 0, 'merged agent branch should be removed when delete flag is set');
 });
 
 test('worktree prune preserves dirty agent worktrees unless --force-dirty is used', () => {
@@ -1558,16 +1563,47 @@ test('worktree prune preserves dirty agent worktrees unless --force-dirty is use
 
   fs.writeFileSync(path.join(worktreePath, 'dirty.txt'), 'dirty\n', 'utf8');
 
-  result = runCmd('bash', ['scripts/agent-worktree-prune.sh'], repoDir);
+  result = runCmd('bash', ['scripts/agent-worktree-prune.sh', '--delete-branches'], repoDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
-  assert.match(result.stdout, /skipped_dirty=1/);
   assert.equal(fs.existsSync(worktreePath), true, 'dirty worktree should remain without --force-dirty');
 
-  result = runCmd('bash', ['scripts/agent-worktree-prune.sh', '--force-dirty'], repoDir);
+  result = runCmd('bash', ['scripts/agent-worktree-prune.sh', '--force-dirty', '--delete-branches'], repoDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
   assert.equal(fs.existsSync(worktreePath), false, 'dirty worktree should be removable with --force-dirty');
 });
 
+test('cleanup command removes merged agent branch/worktree and remote ref', () => {
+  const repoDir = initRepo();
+  seedCommit(repoDir);
+  attachOriginRemote(repoDir);
+
+  let result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['add', '.'], repoDir);
+  assert.equal(result.status, 0, result.stderr);
+  result = runCmd('git', ['commit', '-m', 'apply gx setup'], repoDir, {
+    ALLOW_COMMIT_ON_PROTECTED_BRANCH: '1',
+  });
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['push', 'origin', 'dev'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const worktreePath = path.join(repoDir, '.omx', 'agent-worktrees', 'agent__cleanup-branch');
+  result = runCmd('git', ['worktree', 'add', '-b', 'agent/test-cleanup', worktreePath, 'dev'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  result = runCmd('git', ['-C', worktreePath, 'push', '-u', 'origin', 'agent/test-cleanup'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  result = runNode(['cleanup', '--target', repoDir, '--branch', 'agent/test-cleanup'], repoDir);
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+
+  const localBranch = runCmd('git', ['show-ref', '--verify', '--quiet', 'refs/heads/agent/test-cleanup'], repoDir);
+  assert.notEqual(localBranch.status, 0, 'cleanup should remove local branch');
+  const remoteBranch = runCmd('git', ['ls-remote', '--heads', 'origin', 'agent/test-cleanup'], repoDir);
+  assert.equal(remoteBranch.stdout.trim(), '', 'cleanup should remove remote branch');
+  assert.equal(fs.existsSync(worktreePath), false, 'cleanup should remove worktree');
+});
+
 test('release fails outside the maintainer repo path', () => {
   const repoDir = initRepoOnBranch('main');
   const result = runNode(['release'], repoDir);