Restructure: wiki/ + bibliography consolidation, structure lint (#24)#25
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Key-level audit confirmed every unique key in the 9 root legacy .bib files (and Euclid/Paykari2020.bib) already exists in the canonical bibliography/pyautomemory.bib, so the legacy files are deleted (git history retains them). The pyautopaper.bib back-compat symlink had no live references and is retired. Orphan paper artifacts (ADS-named PDFs and one-file topic folders left over from the 2026-05-22 off-repo PDF sweep) are deleted after verifying canonical coverage; the one gap, Hall 1952 (PhysRev.87.387), gains a canonical entry and its sources TODO section is resolved. index.md no longer instructs committing acquired PDFs — PDFs stay off-repo. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…DE.md wiki/lensing, wiki/smbh, wiki/cti, wiki/methods, wiki/galaxies replace the root-level *_wiki folders (the _wiki suffix is redundant under wiki/). The generic schema is promoted from lensing_wiki/CLAUDE.md to wiki/CLAUDE.md; the lensing wiki keeps a slim scope-only CLAUDE.md like its siblings. Relative links are rewritten for the new depth (append-only log.md files are left as historical record); the citation validator's sources glob and test fixture follow the layout. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…papers scripts/validate_structure.py enforces the layout contract that would have prevented the pre-cleanup state: a top-level allowlist, .bib only under bibliography/, and no paper artifacts (PDF suffix or PDF magic bytes, so extensionless ADS downloads are caught too). Wired into make validate and a minimal GitHub Actions workflow alongside the existing citation validator; the write contract is documented in AGENTS.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Untracked local scratch (.pytest_cache/, in-progress downloads) is out of scope — the layout contract is about what gets committed. Falls back to a filesystem walk outside a git checkout (freshly spawned template). The stale !lensing_wiki/log.md gitignore exception follows the wiki/ move. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
wiki/CLAUDE.md ships verbatim into the PyAutoScientist fresh-slate template (spawn.py KEEP rule); its illustrative examples must not carry instance-content markers, so the SLACS examples become H0LiCOW ones. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Closes #24.
What changed
wiki/layout — the five sub-wikis move towiki/lensing/,wiki/smbh/,wiki/cti/,wiki/methods/,wiki/galaxies/; the shared schema is promoted fromlensing_wiki/CLAUDE.mdtowiki/CLAUDE.mdand the lensing wiki keeps a slim scope-onlyCLAUDE.mdlike its siblings. Relative links rewritten (append-onlylog.mdfiles left as historical record)..bibfiles (andEuclid/Paykari2020.bib) already exists inbibliography/pyautomemory.bib(library.bib: 2918 entries → 1035 unique keys, all present). All legacy bibs deleted (git history retains them); thepyautopaper.bibback-compat symlink retired (no live references).Hubble1926.321H,devaucoleurs1948.247D), the one-file topic folders (CTI/,DarkMatterModels/,Euclid/,LightProFFits/,Medical/),cticomments,euclid.sty. The one canonical-coverage gap, Hall 1952 (PhysRev.87.387), gains a canonical entry and itssources/TODO section is resolved.scripts/validate_structure.py: top-level allowlist,.bibonly underbibliography/, no committed papers (PDF suffix or PDF magic bytes, catching extensionless ADS downloads). Wired intomake validate+ a new CI workflow; write contract documented inAGENTS.md;index.mdno longer instructs committing acquired PDFs.Verification
make validate(citations + structure) green;pytest tests/10/10.make validate+ tests out of the box.🤖 Generated with Claude Code