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

lib/archive.sh

@@ -1,11 +1,17 @@
 #!/bin/bash
-# Branch archiving — archives previous run artifacts when the branch changes.
-# Preserves prd.json, progress.md, and contracts from the previous feature.
+# Run archiving — preserves prd.json, progress.md, and contracts from completed runs.
 #
-# Design: At the end of each run, snapshot_for_archive saves current artifacts
-# to .archive-staging/. On the next run, if the branch changed, check_archive
-# moves the snapshot to archive/ and cleans up. This avoids archiving the
-# WRONG artifacts (the new feature's) when prd.json has already been overwritten.
+# Two archive triggers:
+#   1. Branch change: check_archive detects a new branch and archives the staged snapshot.
+#   2. Completed run: archive_and_reset is called by the /run skill when prd.json shows
+#      all stories passed (or the branch was deleted). This handles the common workflow
+#      of merging a feature branch back to main and starting a new feature.
+#
+# Archive layout:
+#   .loop/archive/
+#     runs.log                          — one-line-per-run index for quick lookup
+#     2026-03-15-auth-system/           — full artifacts from that run
+#       prd.json, progress.md, contracts/
 
 LAST_BRANCH_FILE="$LOOP_DIR/.last-branch"
 STAGING_DIR="$LOOP_DIR/.archive-staging"
@@ -85,5 +91,91 @@ archive_run() {
     rm -f "$LOOP_DIR/progress.md"
     rm -rf "$LOOP_DIR/contracts"
 
+    append_runs_log "$branch_name" "$archive_dir"
     log "Archived previous run to $archive_dir"
 }
+
+# Archive current run artifacts and reset for a new run.
+# Called by the /run skill when a completed run is detected (all stories passed
+# or the feature branch no longer exists). Unlike check_archive (which reads from
+# staging), this archives the LIVE artifacts directly since we know they belong
+# to the completed run.
+archive_and_reset() {
+    local loop_dir="${1:-.loop}"
+    local prd="$loop_dir/prd.json"
+
+    [ -f "$prd" ] || return 0
+
+    # Read branch name from current prd.json
+    local branch_name=""
+    if command -v jq &>/dev/null; then
+        branch_name=$(jq -r '.branchName // empty' "$prd" 2>/dev/null)
+    elif command -v python3 &>/dev/null; then
+        branch_name=$(LOOP_PRD="$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="$loop_dir/archive/$(date +%Y-%m-%d)-${feature_name}"
+    mkdir -p "$archive_dir"
+
+    # Archive live artifacts
+    [ -f "$prd" ] && cp "$prd" "$archive_dir/"
+    [ -f "$loop_dir/progress.md" ] && cp "$loop_dir/progress.md" "$archive_dir/"
+    [ -f "$loop_dir/progress-archive.md" ] && cp "$loop_dir/progress-archive.md" "$archive_dir/"
+    [ -d "$loop_dir/contracts" ] && cp -r "$loop_dir/contracts" "$archive_dir/"
+
+    # Verify archive has content before deleting originals
+    if ! find "$archive_dir" -maxdepth 1 -type f | read -r; then
+        echo "[archive] WARNING: Archive directory is empty — skipping reset to prevent data loss"
+        return 1
+    fi
+
+    append_runs_log "$branch_name" "$archive_dir"
+
+    # Reset run-specific files (keep config.json, init.sh, harness files)
+    rm -f "$loop_dir/prd.json"
+    rm -f "$loop_dir/progress.md"
+    rm -f "$loop_dir/progress-archive.md"
+    rm -rf "$loop_dir/contracts"
+    rm -rf "$loop_dir/.archive-staging"
+    rm -f "$loop_dir/.last-branch"
+    rm -f "$loop_dir/.verdict"
+
+    echo "[archive] Archived completed run to $archive_dir"
+    echo "[archive] .loop/ reset — ready for new stories"
+}
+
+# Append a one-line summary to the runs log.
+append_runs_log() {
+    local branch_name="$1"
+    local archive_dir="$2"
+    local runs_log
+    runs_log="$(dirname "$archive_dir")/runs.log"
+
+    # Read story counts from the archived prd.json
+    local total=0 passed=0 blocked=0
+    local archived_prd="$archive_dir/prd.json"
+    if [ -f "$archived_prd" ]; then
+        if command -v jq &>/dev/null; then
+            total=$(jq '.userStories | length' "$archived_prd" 2>/dev/null || echo 0)
+            passed=$(jq '[.userStories[] | select(.passes == true)] | length' "$archived_prd" 2>/dev/null || echo 0)
+            blocked=$(jq '[.userStories[] | select(.blocked == true)] | length' "$archived_prd" 2>/dev/null || echo 0)
+        elif command -v python3 &>/dev/null; then
+            eval "$(LOOP_PRD="$archived_prd" python3 -c "
+import json, os
+d = json.load(open(os.environ['LOOP_PRD']))
+s = d.get('userStories', [])
+print(f'total={len(s)} passed={sum(1 for x in s if x.get(\"passes\"))} blocked={sum(1 for x in s if x.get(\"blocked\"))}')
+" 2>/dev/null)" || true
+        fi
+    fi
+
+    printf '%s  %-30s  %s/%s passed  %s blocked\n' \
+        "$(date +%Y-%m-%d)" "${branch_name:-unknown}" "$passed" "$total" "$blocked" \
+        >> "$runs_log"
+}