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/BUILD_TREE_PACKAGE_MANIFEST.txt

@@ -0,0 +1,41 @@
+Video-Tree-TRM build-tree related code package
+Source: /home/undergraduate/hyt/Video-Tree-TRM
+Created: 2026-07-06T22:26:58+08:00
+Scope: code/config/scripts/docs/tests needed for building TreeIndex; excludes built trees, videos, frames, logs, experiments, cache, and .env secrets.
+
+Included files:
+  main.py
+  requirements.txt
+  .env.example
+  CLAUDE.md
+  config/default.yaml
+  config/videomme.yaml
+  video_tree_trm/__init__.py
+  video_tree_trm/config.py
+  video_tree_trm/tree_index.py
+  video_tree_trm/text_tree_builder.py
+  video_tree_trm/video_tree_builder.py
+  video_tree_trm/pipeline.py
+  video_tree_trm/llm_client.py
+  video_tree_trm/embeddings.py
+  utils/__init__.py
+  utils/logger_system.py
+  scripts/build_tree_single.py
+  scripts/build_trees_batch.py
+  scripts/build_trees_from_mp4.sh
+  scripts/build_trees_from_urls.sh
+  scripts/build_videomme_trees.sh
+  scripts/download_videos.sh
+  scripts/_download_meta.py
+  docs/architecture.md
+  docs/TD.md
+  docs/EXPERIMENT.md
+  tests/conftest.py
+  tests/unit/test_config.py
+  tests/unit/test_tree_index.py
+  tests/unit/test_text_tree_builder.py
+  tests/unit/test_video_tree_builder.py
+  tests/unit/test_pipeline.py
+  tests/unit/test_embeddings.py
+  tests/unit/test_llm_client.py
+  tests/unit/test_embedding_persistence.py