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/scripts/build_trees_from_mp4.sh

@@ -0,0 +1,87 @@
+#!/usr/bin/env bash
+# =============================================================================
+# build_trees_from_mp4.sh — 从本地 MP4 批量建树（JSON 输出，无 embedding）
+#
+# 用法:
+#   bash scripts/build_trees_from_mp4.sh
+#   bash scripts/build_trees_from_mp4.sh data/videomme/videos/TGom0uiW130.mp4  # 单文件
+#
+# 环境变量:
+#   VIDEO_DIR  — MP4 目录（默认: <PROJECT_ROOT>/data/videomme/videos）
+#   CONFIG     — 配置文件（默认: config/videomme.yaml）
+# =============================================================================
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+PROJECT_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
+
+VIDEO_DIR="${VIDEO_DIR:-${PROJECT_ROOT}/data/videomme/videos}"
+CONFIG="${CONFIG:-${PROJECT_ROOT}/config/videomme.yaml}"
+TREE_DIR="${PROJECT_ROOT}/data/videomme/trees"
+LOG_DIR="${PROJECT_ROOT}/data/videomme/logs"
+LOG="${LOG_DIR}/mp4_build_$(date +%Y%m%d_%H%M%S).log"
+FAILED="${LOG_DIR}/failed_mp4_builds.txt"
+
+mkdir -p "${TREE_DIR}" "${LOG_DIR}"
+
+# 绕过代理
+export NO_PROXY="${NO_PROXY:+${NO_PROXY},}100.83.164.94"
+export no_proxy="${no_proxy:+${no_proxy},}100.83.164.94"
+
+# 激活 conda 环境
+CONDA_BASE="$(conda info --base 2>/dev/null || echo "${HOME}/miniconda3")"
+# shellcheck source=/dev/null
+source "${CONDA_BASE}/etc/profile.d/conda.sh"
+conda activate Video-Tree-TRM
+cd "${PROJECT_ROOT}"
+
+# 确定待处理文件列表
+if [[ $# -gt 0 ]]; then
+    MP4_FILES=("$@")
+else
+    mapfile -t MP4_FILES < <(find "${VIDEO_DIR}" -name "*.mp4" | sort)
+fi
+
+TOTAL=${#MP4_FILES[@]}
+BUILT=0; SKIP=0; FAIL=0
+
+echo "[$(date)] ===== MP4 本地建树开始 =====" | tee "${LOG}"
+echo "[$(date)] 待处理: ${TOTAL} 个视频" | tee -a "${LOG}"
+echo "[$(date)] 配置: ${CONFIG}" | tee -a "${LOG}"
+
+for MP4 in "${MP4_FILES[@]}"; do
+    [[ -z "${MP4}" ]] && continue
+    STEM="$(basename "${MP4}" .mp4)"
+    CACHE="${TREE_DIR}/${STEM}_video.json"
+
+    # 缓存命中跳过
+    if [[ -f "${CACHE}" ]]; then
+        SKIP=$((SKIP+1))
+        echo "[$(date)] [SKIP] ${STEM}" | tee -a "${LOG}"
+        continue
+    fi
+
+    echo "[$(date)] [BUILD] ${STEM}  file=${MP4}" | tee -a "${LOG}"
+
+    if python -u main.py index \
+        --source "${MP4}" \
+        --modality video \
+        --config "${CONFIG}" \
+        >> "${LOG}" 2>&1; then
+        BUILT=$((BUILT+1))
+        echo "[$(date)] [OK]   ${STEM}" | tee -a "${LOG}"
+    else
+        FAIL=$((FAIL+1))
+        echo "[$(date)] [FAIL] ${STEM}" | tee -a "${LOG}"
+        echo "${STEM} ${MP4}" >> "${FAILED}"
+    fi
+done
+
+TREE_COUNT=$(find "${TREE_DIR}" -name "*_video.json" 2>/dev/null | wc -l)
+echo "" | tee -a "${LOG}"
+echo "[$(date)] ===== 汇总 =====" | tee -a "${LOG}"
+echo "[$(date)] 本次新建: ${BUILT}  跳过: ${SKIP}  失败: ${FAIL}" | tee -a "${LOG}"
+echo "[$(date)] 树索引总数: ${TREE_COUNT}" | tee -a "${LOG}"
+[[ ${FAIL} -gt 0 ]] && echo "[$(date)] 失败列表: ${FAILED}" | tee -a "${LOG}"
+echo "[$(date)] 日志: ${LOG}" | tee -a "${LOG}"