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

.claude/scripts/hooks/post-edit-quality.sh

@@ -0,0 +1,83 @@
+#!/usr/bin/env bash
+# ============================================================
+# post-edit-quality.sh
+# Claude Code PostToolUse hook — 每次编辑 .py 文件后自动检查
+#
+# 触发时机：Claude 每次执行 Write/Edit 后
+# 作用：对被修改的文件执行复杂度和风格检查
+# 退出码：0 = 通过，非0 = 报告问题（非阻塞，Claude 会看到反馈）
+#
+# 配置方法：在 .claude/settings.local.json 中注册：
+# "hooks": {
+#   "PostToolUse": [
+#     { "matcher": "Write|Edit", "command": "bash scripts/hooks/post-edit-quality.sh" }
+#   ]
+# }
+# ============================================================
+set -euo pipefail
+
+# <填写: 项目 Conda 环境路径>
+# PROJ_ENV="/home/<user>/miniconda3/envs/<env-name>/bin"
+# [[ -d "$PROJ_ENV" ]] && export PATH="$PROJ_ENV:$PATH"
+
+INPUT=$(cat)
+FILE_PATH=$(echo "$INPUT" | jq -r '.tool_input.file_path // .tool_input.path // ""')
+
+# 只检查 .py 文件
+if [[ ! "$FILE_PATH" == *.py ]]; then
+    exit 0
+fi
+
+# 只检查存在的文件
+if [[ ! -f "$FILE_PATH" ]]; then
+    exit 0
+fi
+
+ERRORS=""
+WARNINGS=""
+
+# ── 1. Ruff 格式 + lint 检查 ──
+if command -v ruff &> /dev/null; then
+    RUFF_OUTPUT=$(ruff check "$FILE_PATH" 2>&1 || true)
+    if [[ -n "$RUFF_OUTPUT" ]]; then
+        ERRORS+="[ruff] 风格/lint 问题：\n$RUFF_OUTPUT\n\n"
+    fi
+fi
+
+# ── 2. Radon 圈复杂度（只报告 C 级及以下） ──
+if command -v radon &> /dev/null; then
+    RADON_OUTPUT=$(radon cc "$FILE_PATH" -n C -s 2>&1 || true)
+    if echo "$RADON_OUTPUT" | grep -qE '^\s+[FMC]\s'; then
+        ERRORS+="[radon] 圈复杂度过高（≥C）：\n$RADON_OUTPUT\n\n"
+    fi
+fi
+
+# ── 3. 文件行数检查（warning，不阻塞）──
+LINE_COUNT=$(wc -l < "$FILE_PATH")
+if [[ "$LINE_COUNT" -gt 200 ]]; then
+    WARNINGS+="[行数] $FILE_PATH 有 ${LINE_COUNT} 行，超过 200 行建议上限。\n\n"
+fi
+
+# ── 4. 禁止裸 except ──
+if grep -nE '^\s*except\s*:\s*$|^\s*except\s+Exception\s*:\s*pass' "$FILE_PATH" 2>/dev/null; then
+    ERRORS+="[安全] 检测到裸 except 或 except Exception: pass，请捕获具体异常类型。\n\n"
+fi
+
+# ── 5. 禁止硬编码敏感信息 ──
+if grep -nEi "(api_key|secret|password|token)\s*=\s*[\"'][^\"']+[\"']" "$FILE_PATH" 2>/dev/null; then
+    ERRORS+="[安全] 疑似硬编码敏感信息，请使用环境变量或 .env 文件。\n\n"
+fi
+
+# ── 输出结果 ──
+if [[ -n "$WARNINGS" ]]; then
+    echo -e "⚠️  Warnings（$FILE_PATH，不阻塞）：\n" >&2
+    echo -e "$WARNINGS" >&2
+fi
+
+if [[ -n "$ERRORS" ]]; then
+    echo -e "❌ 代码质量检查发现问题（$FILE_PATH）：\n" >&2
+    echo -e "$ERRORS" >&2
+    exit 1
+fi
+
+exit 0