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/requirements.txt

@@ -0,0 +1,21 @@
+# 核心
+torch>=2.0
+sentence-transformers>=2.2
+numpy
+
+# LLM/VLM
+openai>=1.0              # 兼容 Qwen/OpenAI/Ollama 接口
+python-dotenv
+
+# 视频处理
+opencv-python
+
+# 配置
+pyyaml
+
+# 测试
+pytest
+pytest-cov
+
+# 代码质量
+ruff