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/config/default.yaml

@@ -0,0 +1,57 @@
+tree:
+  max_paragraphs_per_l2: 5
+  l1_segment_duration: 600.0
+  l2_clip_duration: 60.0
+  l3_fps: 1.0
+  l2_representative_frames: 10
+  cache_dir: "cache/trees"
+  concurrency: 16
+
+embed:
+  backend: "local"                    # "local" (sentence-transformers) | "remote" (OpenAI 兼容 API)
+  model_name: "BAAI/bge-base-zh-v1.5"
+  embed_dim: 2560
+  device: "cuda"
+  api_key: ""                         # 远程模式从 .env 覆盖
+  api_url: ""                         # 远程模式从 .env 覆盖
+
+llm:
+  backend: "qwen"
+  model: "qwen-plus"
+  api_url: "https://dashscope.aliyuncs.com/compatible-mode/v1/chat/completions"
+  max_tokens: 256
+  temperature: 0.1
+  # api_key: 从 .env 加载，此处不写
+
+vlm:
+  backend: "qwen"
+  model: "qwen-vl-plus"
+  api_url: "https://dashscope.aliyuncs.com/compatible-mode/v1/chat/completions"
+  max_tokens: 256
+  temperature: 0.1
+  # api_key: 从 .env 加载，此处不写
+
+retriever:
+  embed_dim: 2560
+  num_heads: 4
+  L_layers: 2
+  L_cycles: 4
+  max_rounds: 5
+  ffn_expansion: 2.0
+  checkpoint: null
+
+train:
+  lr: 1.0e-4
+  weight_decay: 1.0e-5
+  batch_size: 1
+  max_epochs_phase1: 30
+  max_epochs_phase2: 20
+  nav_loss_weight: 1.0
+  act_loss_weight: 0.1
+  margin_loss_weight: 0.5
+  act_lambda_step: 0.1
+  act_gamma: 0.9
+  eval_interval: 5
+  save_dir: "checkpoints"
+  dataset: "longbench"
+  dataset_path: "data/longbench"