diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json
index bb97044..0540187 100644
--- a/.claude-plugin/marketplace.json
+++ b/.claude-plugin/marketplace.json
@@ -10,7 +10,7 @@
       "name": "agent-loop",
       "source": "./",
       "description": "Autonomous generator-evaluator agent loop for long-running coding tasks. Plan interactively, then execute with full visibility.",
-      "version": "0.8.0",
+      "version": "0.9.0",
       "author": {
         "name": "Sheldon"
       },
diff --git a/.claude-plugin/plugin.json b/.claude-plugin/plugin.json
index 3bf91e8..b4b1971 100644
--- a/.claude-plugin/plugin.json
+++ b/.claude-plugin/plugin.json
@@ -1,6 +1,6 @@
 {
   "name": "agent-loop",
-  "version": "0.8.0",
+  "version": "0.9.0",
   "description": "Autonomous generator-evaluator agent loop for long-running coding tasks. Run /agent-loop:run to start.",
   "author": {
     "name": "Sheldon"
diff --git a/lib/archive.sh b/lib/archive.sh
index d67d123..8bca8a3 100644
--- a/lib/archive.sh
+++ b/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" \
+        >> "$runs_log"
+}
diff --git a/setup.sh b/setup.sh
index 887927c..1e05fa9 100755
--- a/setup.sh
+++ b/setup.sh
@@ -57,9 +57,17 @@ PROJECT_ROOT="$(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"
diff --git a/skills/run/SKILL.md b/skills/run/SKILL.md
index de6ab2c..142d0ff 100644
--- a/skills/run/SKILL.md
+++ b/skills/run/SKILL.md
@@ -44,7 +44,38 @@ Show the output. If setup fails, stop.
 
 Check if `.loop/prd.json` exists.
 
-**If it does NOT exist**, generate it:
+**If it exists**, check whether the previous run is complete. Run:
+
+```bash
+source .loop/lib/state.sh 2>/dev/null; LOOP_DIR=.loop all_stories_pass 2>/dev/null && echo "ALL_PASSED" || echo "IN_PROGRESS"
+```
+
+Also check if the feature branch from prd.json still exists:
+
+```bash
+jq -r '.branchName // empty' .loop/prd.json
+```
+
+If the result is `ALL_PASSED` **or** the branch no longer exists (deleted after merge), the previous run is done. Archive it and reset:
+
+```bash
+LOOP_DIR=.loop source .loop/lib/state.sh && source .loop/lib/archive.sh && archive_and_reset .loop
+```
+
+Tell the user: *"Archived previous run ({branch}). Starting fresh."*
+
+Then proceed to generate new stories below.
+
+If the result is `IN_PROGRESS` and the branch still exists, the previous run is still active. Tell the user:
+
+> **Existing run found** — {passed}/{total} stories complete on `{branch}`.
+>
+> - Say **go** to resume the existing run
+> - Say **archive** to archive this run and start fresh
+
+Wait for the user to decide before proceeding.
+
+**If `prd.json` does NOT exist**, generate it:
 
 1. Search for existing specs or plans:
    - `docs/superpowers/specs/*.md`
diff --git a/skills/stories/SKILL.md b/skills/stories/SKILL.md
index 0bb23da..bdb2c24 100644
--- a/skills/stories/SKILL.md
+++ b/skills/stories/SKILL.md
@@ -13,6 +13,20 @@ Dispatch the planner agent to decompose a spec into stories. The planner agent c
 
 Verify `.loop/config.json` exists. If not, tell the user to run `/agent-loop:setup` first and stop.
 
+If `.loop/prd.json` already exists, check whether the previous run is complete:
+
+```bash
+source .loop/lib/state.sh 2>/dev/null; LOOP_DIR=.loop all_stories_pass 2>/dev/null && echo "ALL_PASSED" || echo "IN_PROGRESS"
+```
+
+If `ALL_PASSED`, archive the completed run before generating new stories:
+
+```bash
+LOOP_DIR=.loop source .loop/lib/state.sh && source .loop/lib/archive.sh && archive_and_reset .loop
+```
+
+If `IN_PROGRESS`, warn the user that a run is active and ask whether to archive it or abort.
+
 ### 2. Find the spec
 
 Check these locations: