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/tools/deepxiv_fetch.py

@@ -0,0 +1,52 @@
+"""DeepXiv CLI 的轻量适配器。"""
+
+from __future__ import annotations
+
+import argparse
+import shutil
+import subprocess
+import sys
+from typing import cast
+
+if shutil.which("deepxiv") is None:
+    print("警告: 未找到 deepxiv CLI，已跳过 DeepXiv 适配器。", file=sys.stderr)
+    sys.exit(0)
+
+
+def _run_deepxiv(arguments: list[str]) -> int:
+    """调用底层 deepxiv 命令并透传输出。"""
+    completed = subprocess.run(["deepxiv", *arguments], check=False)
+    return completed.returncode
+
+
+def build_parser() -> argparse.ArgumentParser:
+    """构建命令行参数解析器。"""
+    parser = argparse.ArgumentParser(description="DeepXiv 命令适配器")
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    for command_name in ("search", "paper-brief", "paper-head", "paper-section"):
+        subparser = subparsers.add_parser(
+            command_name, help=f"转发 deepxiv {command_name} 命令"
+        )
+        subparser.add_argument(
+            "args", nargs=argparse.REMAINDER, help="透传给 deepxiv 的参数"
+        )
+
+    return parser
+
+
+def main(argv: list[str] | None = None) -> int:
+    """CLI 入口。"""
+    parser = build_parser()
+    args = parser.parse_args(argv)
+
+    try:
+        command_args = [args.command, *cast(list[str], args.args)]
+        return _run_deepxiv(command_args)
+    except OSError as exc:
+        print(f"错误: {exc}", file=sys.stderr)
+        return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())