feat: worktree-based run isolation for parallel loops

Each /agent-loop:run now creates a git worktree for the feature branch
before generating stories. This provides full isolation:

- Multiple loops can run in parallel on different specs in the same project
- Main working directory stays on main, always available
- Each worktree has its own .loop/ state, tmux session, and branch
- Completed runs are archived to main's .loop/archive/ with runs.log

Changes:
- setup.sh: add --init-worktree mode for initializing worktree .loop/
- archive.sh: add archive_from_worktree() for cross-directory archiving
- loop.sh: replace branch checkout with validation (worktree is pre-checked-out)
- agents/planner.md: accept absolute path prefix for worktree .loop/ writes
- skills/run/SKILL.md: full rewrite — worktree creation in Phase 2, launch in
  Phase 3, archive on completion, .active-worktree tracking file
- skills/stories/SKILL.md: worktree-aware, defer to /run for full flow

Bump to 0.12.0.

setup.sh

@@ -11,16 +11,30 @@
 set -euo pipefail
 
 # --- Parse arguments ---
-UPDATE_ONLY=false
+ACTION="scaffold"
 MODE="${1:-implement}"
+WORKTREE_PATH=""
+MAIN_LOOP_DIR=""
 
-if [ "$MODE" = "--update" ]; then
-    UPDATE_ONLY=true
-    MODE="${2:-implement}"  # mode not used in update, but keep arg parsing clean
-fi
+case "$MODE" in
+    --update)
+        ACTION="update"
+        MODE="${2:-implement}"
+        ;;
+    --init-worktree)
+        ACTION="init-worktree"
+        WORKTREE_PATH="$2"
+        MAIN_LOOP_DIR="$3"
+        if [ -z "$WORKTREE_PATH" ] || [ -z "$MAIN_LOOP_DIR" ]; then
+            echo "[setup] ERROR: --init-worktree requires <worktree_path> <main_loop_dir>"
+            echo "[setup] Usage: setup.sh --init-worktree /path/to/worktree /path/to/main/.loop"
+            exit 1
+        fi
+        ;;
+esac
 
 # --- Validate mode ---
-if [ "$UPDATE_ONLY" = false ] && [[ ! "$MODE" =~ ^(implement|explore|fix)$ ]]; then
+if [ "$ACTION" = "scaffold" ] && [[ ! "$MODE" =~ ^(implement|explore|fix)$ ]]; then
     echo "[setup] ERROR: Invalid mode '$MODE'. Must be: implement, explore, fix"
     exit 1
 fi
@@ -63,7 +77,7 @@ if [ -f "$HARNESS_SRC/.claude-plugin/plugin.json" ]; then
 fi
 
 # --- Update-only mode: refresh harness files without touching run state ---
-if [ "$UPDATE_ONLY" = true ]; then
+if [ "$ACTION" = "update" ]; then
     LOOP_DIR="$(pwd)/.loop"
     if [ ! -d "$LOOP_DIR" ]; then
         echo "[setup] ERROR: No .loop/ directory found. Run setup first."
@@ -83,6 +97,34 @@ if [ "$UPDATE_ONLY" = true ]; then
     exit 0
 fi
 
+# --- Init-worktree mode: initialize .loop/ in a worktree from main's config ---
+if [ "$ACTION" = "init-worktree" ]; then
+    LOOP_DIR="$WORKTREE_PATH/.loop"
+    mkdir -p "$LOOP_DIR"
+
+    # Copy harness files from plugin source
+    cp -r "$HARNESS_SRC/prompts"    "$LOOP_DIR/"
+    cp -r "$HARNESS_SRC/templates"  "$LOOP_DIR/"
+    cp -r "$HARNESS_SRC/lib"        "$LOOP_DIR/"
+    cp    "$HARNESS_SRC/loop.sh"    "$LOOP_DIR/"
+    chmod +x "$LOOP_DIR/loop.sh"
+
+    # Copy project config and init from main's .loop/
+    [ -f "$MAIN_LOOP_DIR/config.json" ] && cp "$MAIN_LOOP_DIR/config.json" "$LOOP_DIR/"
+    [ -f "$MAIN_LOOP_DIR/init.sh" ] && cp "$MAIN_LOOP_DIR/init.sh" "$LOOP_DIR/"
+
+    # Stamp harness version
+    [ -n "$PLUGIN_VERSION" ] && echo "$PLUGIN_VERSION" > "$LOOP_DIR/.harness-version"
+
+    # Create .gitignore for worktree's .loop/
+    cat > "$LOOP_DIR/.gitignore" << 'GITIGNORE'
+*
+GITIGNORE
+
+    echo "[setup] Worktree .loop/ initialized at $LOOP_DIR"
+    exit 0
+fi
+
 # --- Ensure git repo exists ---
 if ! git rev-parse --git-dir &>/dev/null; then
     echo "[setup] No git repo found. Initializing..."
@@ -141,6 +183,7 @@ archive/
 .archive-staging/
 .last-branch
 .harness-version
+.active-worktree
 .loop.lock
 GITIGNORE