v0.4.21: fix #422 cluster-only KeyError total_files, fix #423 --update drops existing nodes

graphify/__main__.py

@@ -1308,7 +1308,8 @@ def main() -> None:
         questions = suggest_questions(G, communities, labels)
         tokens = {"input": 0, "output": 0}
         report = generate(G, communities, cohesion, labels, gods, surprises,
-                          {}, tokens, str(watch_path), suggested_questions=questions)
+                          {"warning": "cluster-only mode — file stats not available"},
+                          tokens, str(watch_path), suggested_questions=questions)
         out = watch_path / "graphify-out"
         (out / "GRAPH_REPORT.md").write_text(report, encoding="utf-8")
         to_json(G, communities, str(out / "graph.json"))

graphify/skill.md

@@ -862,6 +862,17 @@ if deleted:
 # Merge: new nodes/edges into existing graph
 G_existing.update(G_new)
 print(f'Merged: {G_existing.number_of_nodes()} nodes, {G_existing.number_of_edges()} edges')
+
+# Write merged result back to .graphify_extract.json so Step 4 sees the full graph
+merged_out = {
+    'nodes': [{'id': n, **d} for n, d in G_existing.nodes(data=True)],
+    'edges': [{'source': u, 'target': v, **d} for u, v, d in G_existing.edges(data=True)],
+    'hyperedges': new_extraction.get('hyperedges', []),
+    'input_tokens': new_extraction.get('input_tokens', 0),
+    'output_tokens': new_extraction.get('output_tokens', 0),
+}
+Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out))
+print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')
 " 
 ```