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/systematic-debugging/test-academic.md

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+# Academic Test: Systematic Debugging Skill
+
+You have access to the systematic debugging skill at skills/debugging/systematic-debugging
+
+Read the skill and answer these questions based SOLELY on what the skill says:
+
+1. What are the four phases of systematic debugging?
+2. What must you do BEFORE attempting any fix?
+3. In Phase 3, what should you do if your first hypothesis doesn't work?
+4. What does the skill say about fixing multiple things at once?
+5. What should you do if you don't fully understand the issue?
+6. Is it ever acceptable to skip the process for simple bugs?
+
+Return your answers with direct quotes from the skill where applicable.