Restore missing branch-start assets so doctor branches can finish safely (#43)

Repeated gx doctor sandboxes were left dirty because essential guardex-managed entries were absent and had to be regenerated each run. This commit captures those repairs so new doctor branches stop repeating the same drift.

Constraint: Keep protected main read-only; changes must flow through agent branch PR

Rejected: Drop doctor-generated changes locally per run | branch state keeps regressing

Confidence: medium

Scope-risk: narrow

Reversibility: clean

Directive: If doctor keeps recreating the same files, merge the first repair branch before rerunning doctor

Tested: gx scan output before/after doctor on main workspace

Not-tested: full npm test suite

Co-authored-by: NagyVikt <nagy.viktordp@gmail.com>

Author: NagyVikt

.gitignore

@@ -12,7 +12,7 @@ scripts/install-agent-git-hooks.sh
 scripts/openspec/init-plan-workspace.sh
 .githooks/pre-commit
 oh-my-codex/
-.codex/skills/musafety/SKILL.md
-.claude/commands/musafety.md
+.codex/skills/guardex/SKILL.md
+.claude/commands/guardex.md
 .omx/state/agent-file-locks.json
 # multiagent-safety:END

package.json

@@ -15,7 +15,7 @@
     "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 --base dev",
+    "agent:cleanup": "gx 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",

scripts/agent-branch-start.sh

@@ -1,16 +1,14 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-TASK_NAME="${1:-task}"
-AGENT_NAME="${2:-agent}"
-BASE_BRANCH="${3:-}"
+TASK_NAME="task"
+AGENT_NAME="agent"
+BASE_BRANCH=""
 BASE_BRANCH_EXPLICIT=0
 WORKTREE_MODE=1
+ALLOW_IN_PLACE=0
 WORKTREE_ROOT_REL=".omx/agent-worktrees"
-
-if [[ -n "${3:-}" ]]; then
-  BASE_BRANCH_EXPLICIT=1
-fi
+POSITIONAL_ARGS=()
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
@@ -31,25 +29,53 @@ while [[ $# -gt 0 ]]; do
       WORKTREE_MODE=0
       shift
       ;;
+    --allow-in-place)
+      ALLOW_IN_PLACE=1
+      shift
+      ;;
     --worktree-root)
       WORKTREE_ROOT_REL="${2:-.omx/agent-worktrees}"
       shift 2
       ;;
     --)
       shift
+      while [[ $# -gt 0 ]]; do
+        POSITIONAL_ARGS+=("$1")
+        shift
+      done
       break
       ;;
     -*)
       echo "[agent-branch-start] Unknown option: $1" >&2
-      echo "Usage: $0 [task] [agent] [base] [--in-place] [--worktree-root <path>]" >&2
+      echo "Usage: $0 [task] [agent] [base] [--in-place --allow-in-place] [--worktree-root <path>]" >&2
       exit 1
       ;;
     *)
-      break
+      POSITIONAL_ARGS+=("$1")
+      shift
       ;;
   esac
 done
 
+if [[ "${#POSITIONAL_ARGS[@]}" -gt 3 ]]; then
+  echo "[agent-branch-start] Too many positional arguments." >&2
+  echo "Usage: $0 [task] [agent] [base] [--in-place --allow-in-place] [--worktree-root <path>]" >&2
+  exit 1
+fi
+
+if [[ "${#POSITIONAL_ARGS[@]}" -ge 1 ]]; then
+  TASK_NAME="${POSITIONAL_ARGS[0]}"
+fi
+
+if [[ "${#POSITIONAL_ARGS[@]}" -ge 2 ]]; then
+  AGENT_NAME="${POSITIONAL_ARGS[1]}"
+fi
+
+if [[ "${#POSITIONAL_ARGS[@]}" -ge 3 ]]; then
+  BASE_BRANCH="${POSITIONAL_ARGS[2]}"
+  BASE_BRANCH_EXPLICIT=1
+fi
+
 sanitize_slug() {
   local raw="$1"
   local fallback="${2:-task}"
@@ -180,6 +206,12 @@ if git show-ref --verify --quiet "refs/heads/${branch_name}"; then
 fi
 
 if [[ "$WORKTREE_MODE" -eq 0 ]]; then
+  if [[ "$ALLOW_IN_PLACE" -ne 1 ]]; then
+    echo "[agent-branch-start] --in-place is blocked by default to prevent accidental edits on protected branches." >&2
+    echo "[agent-branch-start] If you really need it, pass both: --in-place --allow-in-place" >&2
+    exit 1
+  fi
+
   if ! git diff --quiet || ! git diff --cached --quiet; then
     echo "[agent-branch-start] Working tree is not clean. Commit/stash changes before starting an in-place branch." >&2
     exit 1