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.

lib/archive.sh

@@ -150,6 +150,54 @@ print(json.load(open(os.environ['LOOP_PRD'])).get('branchName', ''), end='')
     echo "[archive] .loop/ reset — ready for new stories"
 }
 
+# Archive a completed run from a worktree back to the main project's .loop/archive/.
+# Called by the /run skill's completion handler after the loop finishes in a worktree.
+#
+# Usage: archive_from_worktree <worktree_loop_dir> <main_loop_dir>
+#   worktree_loop_dir: absolute path to the worktree's .loop/ (source)
+#   main_loop_dir:     absolute path to the main project's .loop/ (destination)
+archive_from_worktree() {
+    local wt_loop_dir="$1"
+    local main_loop_dir="$2"
+    local wt_prd="$wt_loop_dir/prd.json"
+
+    [ -f "$wt_prd" ] || { echo "[archive] WARNING: No prd.json in worktree — nothing to archive"; return 1; }
+
+    # Read branch name from worktree's prd.json
+    local branch_name=""
+    if command -v jq &>/dev/null; then
+        branch_name=$(jq -r '.branchName // empty' "$wt_prd" 2>/dev/null)
+    elif command -v python3 &>/dev/null; then
+        branch_name=$(LOOP_PRD="$wt_prd" python3 -c "
+import json, os
+print(json.load(open(os.environ['LOOP_PRD'])).get('branchName', ''), end='')
+" 2>/dev/null)
+    fi
+
+    local feature_name
+    feature_name=$(echo "${branch_name:-unknown}" | sed 's|.*/||')
+
+    local archive_dir="$main_loop_dir/archive/$(date +%Y-%m-%d)-${feature_name}"
+    mkdir -p "$archive_dir"
+
+    # Copy artifacts from worktree
+    [ -f "$wt_prd" ] && cp "$wt_prd" "$archive_dir/"
+    [ -f "$wt_loop_dir/progress.md" ] && cp "$wt_loop_dir/progress.md" "$archive_dir/"
+    [ -f "$wt_loop_dir/progress-archive.md" ] && cp "$wt_loop_dir/progress-archive.md" "$archive_dir/"
+    [ -d "$wt_loop_dir/contracts" ] && cp -r "$wt_loop_dir/contracts" "$archive_dir/"
+    [ -d "$wt_loop_dir/triage" ] && cp -r "$wt_loop_dir/triage" "$archive_dir/"
+
+    # Verify archive has content
+    if ! find "$archive_dir" -maxdepth 1 -type f | read -r; then
+        echo "[archive] WARNING: Archive directory is empty — copy may have failed"
+        return 1
+    fi
+
+    append_runs_log "$branch_name" "$archive_dir"
+
+    echo "[archive] Archived worktree run to $archive_dir"
+}
+
 # Append a one-line summary to the runs log.
 append_runs_log() {
     local branch_name="$1"