chore(graphify): bump skill to v0.4.23

Auto-upgraded during /graphify invocation. Notable SKILL.md changes:
safer AST cache_root (pin to cwd), clearer node ID format docs with
concrete example, new Step 6b Wiki export (opt-in via --wiki),
--update now persists merged extraction back to .graphify_extract.json
so Step 4 sees the full graph.

Co-Authored-By: Claude <noreply@anthropic.com>

skills/graphify/.graphify_version

@@ -1 +1 @@
-0.4.2
+0.4.23

skills/graphify/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: graphify
-description: any input (code, docs, papers, images) → knowledge graph → clustered communities → HTML + JSON + audit report
+description: "any input (code, docs, papers, images) - knowledge graph - clustered communities - HTML + JSON + audit report"
 trigger: /graphify
 ---
 
@@ -185,7 +185,7 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files)
+    result = extract(code_files, cache_root=Path('.'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2))
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
@@ -299,8 +299,10 @@ confidence_score is REQUIRED on every edge - never omit it, never use 0.5 as a d
   Weak or speculative: 0.4-0.5. Most edges should be 0.6-0.9, not 0.5.
 - AMBIGUOUS edges: 0.1-0.3
 
+Node ID format: lowercase, only `[a-z0-9_]`, no dots or slashes. Format: `{stem}_{entity}` where stem is the filename without extension and entity is the symbol name, both normalized (lowercase, non-alphanumeric chars replaced with `_`). Example: `src/auth/session.py` + `ValidateToken` → `session_validatetoken`. This must match the ID the AST extractor generates so cross-references between code and semantic nodes connect correctly.
+
 Output exactly this JSON (no other text):
-{"nodes":[{"id":"filestem_entityname","label":"Human Readable Name","file_type":"code|document|paper|image","source_file":"relative/path","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"relative/path","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"relative/path"}],"input_tokens":0,"output_tokens":0}
+{"nodes":[{"id":"session_validatetoken","label":"Human Readable Name","file_type":"code|document|paper|image","source_file":"relative/path","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"relative/path","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"relative/path"}],"input_tokens":0,"output_tokens":0}
 ```
 
 **Step B3 - Collect, cache, and merge**
@@ -548,6 +550,36 @@ else:
 "
 ```
 
+### Step 6b - Wiki (only if --wiki flag)
+
+**Only run this step if `--wiki` was explicitly given in the original command.**
+
+Run this before Step 9 (cleanup) so `.graphify_labels.json` is still available.
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import json
+from graphify.build import build_from_json
+from graphify.wiki import to_wiki
+from graphify.analyze import god_nodes
+from pathlib import Path
+
+extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text())
+analysis   = json.loads(Path('graphify-out/.graphify_analysis.json').read_text())
+labels_raw = json.loads(Path('graphify-out/.graphify_labels.json').read_text()) if Path('graphify-out/.graphify_labels.json').exists() else {}
+
+G = build_from_json(extraction)
+communities = {int(k): v for k, v in analysis['communities'].items()}
+cohesion = {int(k): v for k, v in analysis['cohesion'].items()}
+labels = {int(k): v for k, v in labels_raw.items()}
+gods = god_nodes(G)
+
+n = to_wiki(G, communities, 'graphify-out/wiki', community_labels=labels or None, cohesion=cohesion, god_nodes_data=gods)
+print(f'Wiki: {n} articles written to graphify-out/wiki/')
+print('  graphify-out/wiki/index.md  ->  agent entry point')
+"
+```
+
 ### Step 7 - Neo4j export (only if --neo4j or --neo4j-push flag)
 
 **If `--neo4j`** - generate a Cypher file for manual import:
@@ -830,6 +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)')
 " 
 ```