feat: auto-archive completed runs before starting new features

When /agent-loop:run detects a previous run with all stories passed (or the
feature branch deleted after merge), it archives the old artifacts and resets
.loop/ automatically — no more manual rm -rf .loop.

- Add archive_and_reset() for on-demand archiving from skills
- Add runs.log index tracking all archived runs
- Update /run and /stories skills to detect completed runs
- setup.sh archives instead of hard-failing when prd.json exists
- Bump version to 0.9.0

setup.sh

@@ -57,9 +57,17 @@ PROJECT_ROOT="$(pwd)"
 LOOP_DIR="$PROJECT_ROOT/.loop"
 
 if [ -d "$LOOP_DIR" ] && [ -f "$LOOP_DIR/prd.json" ]; then
-    echo "[setup] .loop/ already exists with prd.json."
-    echo "[setup] To re-initialize, delete .loop/ first: rm -rf .loop"
-    exit 1
+    echo "[setup] .loop/ already exists with prd.json — archiving previous run..."
+    # Source state.sh (needed by archive.sh for story queries) and archive.sh
+    LOOP_DIR="$LOOP_DIR" source "$LOOP_DIR/lib/state.sh" 2>/dev/null || true
+    LOOP_DIR="$LOOP_DIR" source "$LOOP_DIR/lib/archive.sh" 2>/dev/null || true
+    if type archive_and_reset &>/dev/null; then
+        archive_and_reset "$LOOP_DIR"
+    else
+        # Fallback for old harness versions without archive_and_reset
+        echo "[setup] WARNING: Could not archive (old harness version). To re-initialize, delete .loop/ first: rm -rf .loop"
+        exit 1
+    fi
 fi
 
 mkdir -p "$LOOP_DIR"