chore: track claude skills, tools, templates, reference code and research-wiki

- Add all claude skills (brainstorming, commit, debugging, TDD, etc.)
- Add claude hooks (pre-commit-guard, post-edit-quality)
- Add research templates (experiment plan, research brief, etc.)
- Add claude tools (arxiv/semantic_scholar/openalex fetch, wiki, exa)
- Add TRM4 reference implementation as algorithm fidelity baseline
- Add research-wiki content (plans, index, graph, query_pack)
- Update .gitignore to exclude .graphify_version runtime state

research-wiki/graph/edges.json

@@ -0,0 +1,11 @@
+{
+  "directed": true,
+  "nodes": [
+    {
+      "id": "plan:infrastructure-setup",
+      "label": "项目基础设施初始化计划",
+      "type": "plan"
+    }
+  ],
+  "links": []
+}