Add pre-registration draft, timeline skeleton and AI-use log

Claude-Session: https://claude.ai/code/session_01S8KN7NuUCm8nXLmy6eDuVv

AI-USE-LOG.md

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+# GenAI use log
+
+Record of significant AI-assisted sessions on the thesis, as with the CS6513 notebook's
+transparency log. `[Check the thesis handbook's GenAI policy and adjust this format to match.]`
+
+| Date | Tool | What it did | What I (Cormac) decided / checked |
+|---|---|---|---|
+| 28/10/2026 | Claude Code (Opus 5.5) | Organised files into `thesis/` + git. Generated `references.bib` from arXiv metadata and found reference errors in the CS6513 paper (`citation-check.md`). Wrote literature-search scripts; ran logged searches (OpenAlex, arXiv) and one snowball round (Semantic Scholar); drafted `protocol.md`; made a first-pass title/abstract screening suggestion (`ai_proposal` column). Set up nanoGPT + TinyStories + run logging (`06-experiments/`); added the `qk_norm` flag; ran 4 smoke-test runs. Drafted `preregistration.md` and `timeline.md` skeletons | `[Your note]` |