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

reference/.env.example

@@ -0,0 +1,11 @@
+# .env — 敏感信息，不提交到 Git
+LLM_API_KEY=
+LLM_MODEL=
+LLM_API_URL=
+VLM_API_KEY=
+VLM_MODEL=
+VLM_API_URL=
+EMBED_BACKEND=
+EMBED_MODEL=
+EMBED_API_KEY=
+EMBED_API_URL=