Restructure: wiki/ + bibliography consolidation, structure lint, template sync #24

Affected Repositories

• PyAutoMemory (primary)
• PyAutoMind (scripts/spawn.py template manifest + prose)
• PyAutoBrain (one-line memory-faculty glob + one doc mention — small parallel PR; repo is claimed by the in-flight workspace-agent task, parallel PR explicitly user-approved, no file overlap)
• PyAutoLabs root AGENTS.md + admin_jammy docs (trivial pointer edits at ship time)
• PyAutoScientist (docs follow-up only; not part of this PR set)

Branch Survey

Suggested branch: feature/memory-structure-cleanup
Worktree root: ~/Code/PyAutoLabs-wt/memory-structure-cleanup/ (created by /start_library)
Work classification: infrastructure (organ repos; library-dev worktree mechanics)

Implementation Steps

1. Bib audit (read-only first). Script a key extraction over the 9 root .bib files + Euclid/Paykari2020.bib; diff key sets (and DOI/arXiv/title matches via bibliography/bibkey_aliases.yaml conventions) against bibliography/pyautomemory.bib. Report: per-file unique-key count. Fold verified missing entries into canonical (respecting the existing "conflicts never replace the library.bib-derived entry" precedent). Run make validate-literature-citations.
2. Delete legacy bib files (post-fold): cooper.bib, library.bib, library2.bib, library_jam.bib, libraryipft.bib, manual.bib, pyautofit.bib, pyautolens.bib, qiuhan.bib, bibliography/pyautopaper.bib symlink.
3. Retire strays: verify/add canonical entries + source stubs for the six orphan papers; delete Hubble1926.321H, devaucoleurs1948.247D, CTI/, DarkMatterModels/, Euclid/, LightProFFits/, Medical/, cticomments, euclid.sty.
4. Wiki move: git mv <domain>_wiki wiki/<domain> for lensing/smbh/cti/methods/galaxies; git mv wiki/lensing/CLAUDE.md wiki/CLAUDE.md (schema is shared, sub-wikis inherit); scripted rewrite of relative links (../<d>_wiki/ → ../<d>/, <d>_wiki/ → wiki/<d>/ in root files); update index.md, README.md, AGENTS.md, bibliography/README.md.
5. Validator + lint: update scripts/validate_literature_citations.py glob (*_wiki/sources → wiki/*/sources); add structure lint (new scripts/validate_structure.py or extend existing): top-level allowlist, no .bib outside bibliography/, no PDF/binary blobs; Makefile target; minimal GitHub Actions workflow running make validate-literature-citations + the lint; update tests/.
6. Rules prose: AGENTS.md + CONTRIBUTING.md — the layout contract (wiki/ + bibliography/ + allowlisted root files), PDFs off-repo, new bib entries only in canonical. Fix index.md reading-queue instruction (stub + cite; never commit the PDF).
7. PyAutoMind: update scripts/spawn.py manifest (*_wiki/* → wiki/* rules; keep bibliography/* EMPTY, *.bib DROP) + generated prose (example_wiki/ → wiki/example/); run /spawn drift check (dry-run) — actual template republish is a separate human-confirmed step.
8. PyAutoBrain (small parallel PR): agents/faculties/memory/_memory.py glob("*_wiki") → also/instead wiki/* (tolerate both layouts for one release); update skills/sampler_pipeline/reference.md mention (PyAutoMemory/methods_wiki → PyAutoMemory/wiki/methods).
9. Ship-time pointer edits: workspace-root AGENTS.md science pointer (sub-wiki names), admin_jammy/claude.md + README.md mentions.
10. Research tail: design-note comment on this issue — canonical-key TODO sweep (345 open TODOs; the legacy fold should resolve some), a memory-surface manifest for the faculty ("no layout coupling" promise), reading-queue lifecycle, single canonical bib vs per-domain shards (recommend single), repo weight (legacy blobs remain in git history; no rewrites, template spawn is the clean-slate path). File accepted follow-ups via intake, one at a time.

Key Files

• PyAutoMemory/bibliography/pyautomemory.bib — canonical bib; fold target
• PyAutoMemory/bibliography/README.md — bib policy; update legacy-inputs paragraph once legacy files are gone
• PyAutoMemory/scripts/validate_literature_citations.py — glob("*_wiki/sources") layout coupling
• PyAutoMemory/index.md, README.md, AGENTS.md — navigation + rules
• PyAutoMemory/lensing_wiki/CLAUDE.md — shared schema (promote to wiki/CLAUDE.md)
• PyAutoMind/scripts/spawn.py — fresh-slate template manifest (*_wiki/* DROP, bibliography/* EMPTY, *.bib DROP) + template prose
• PyAutoBrain/agents/faculties/memory/_memory.py — glob("*_wiki") (line 35)
• PyAutoBrain/skills/sampler_pipeline/reference.md — methods_wiki mention

PyAutoMemory, This feels like it could be cleaned up:

• Have a wiki/ folder with the wikis, analgous to autolens_assistant, at the moment the wiki fodlers seem scattered.
• Fodlers like CTI, DarkMatterModels, Euclid and LightProfFits contain individual .pdf files or .bib files. These must be
  some sort of unused hangover from previous work which can be removed?
• Is bibliography/pyautopaper.bib now redundant?
• There are like 9 .bib files in the main repo, I am sure I just dumped them here but its time to clean them up. Either
  consolidate to one .bib file or have a bib folder next to wiki which puts the .bib entries in sensible standalone files.
  I know bib referencing is hard for AI so these do contain important info so dont just delete some, but also remove duplication.
• devaucoleurs1948.247D and Hubble1926.321H surely
  dont belong here?

In general, it feels like some rules need to be put in place across PyAutoScientist to prevent PyAutoMemory
from ending up in this statem and it would benefit from a bit more structure (e.g. the wikis folder, bib folder)
to make it more navigateable for a random user. This structure would also generalize it and make it more useable
for anyone in the PyAutoScientist ecosystem, especially as then theyd just need empty wiki, bib folders and
whatnot.

Finally do deep research and think hard about any other longer term changes we can make to the structure and
design of PyAutoMemory.