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/skills/commit/SKILL.md

@@ -0,0 +1,68 @@
+---
+name: commit
+description: Use when committing code changes - enforces commit message format, safety checks, and prohibits AI signatures
+---
+
+# Commit
+
+Automatically generate a commit message and submit the code.
+
+## Workflow
+
+1. **Check status**: run `git status` to inspect changes (do not use `-uall`)
+2. **Review diff**: run `git diff --staged` and `git diff` to inspect the exact changes
+3. **Check style**: run `git log --oneline -10` to review recent commit style
+4. **Generate message**: create a commit message that follows the rules below
+5. **Commit**: stage the files and commit
+
+## Commit Message Rules
+
+### Format
+```text
+<type>: <description>
+
+[optional body]
+```
+
+### Type Values
+- `feat`: new feature
+- `fix`: bug fix
+- `docs`: documentation update
+- `refactor`: refactor with no functional change
+- `test`: test-related change
+- `chore`: build / tooling / configuration
+- `perf`: performance optimization
+- `ci`: CI/CD related
+
+### Rules
+- The description must be written in English
+- Keep it under 72 characters
+- Use the imperative mood, for example "add user authentication" instead of "added user authentication"
+
+## Safety Rules
+
+> [!CAUTION]
+> **Never** add any AI signature to a commit message:
+> - Do not add `Co-Authored-By: Claude`
+> - Do not add `🤖 Generated with...`
+> - Do not add any AI signature or marker
+
+## Sensitive File Check
+
+Before committing, check whether any of the following files were accidentally added:
+- `.env` / `.env.*`
+- `credentials.json`
+- `*_secret*`
+- `*.pem` / `*.key`
+
+If sensitive files are found, **warn the user** and wait for confirmation.
+
+## Examples
+
+```bash
+# Auto-generate a message
+/commit
+
+# Specify a message
+/commit "feat: add user login"
+```