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Restructure: descriptive tier and experiment names, paper/manuscript

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- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
  (imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
  they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
  where they feed none; configs keep their `experiment:` value so parquet
  hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
  SI Methods/tables updated; make clean no longer deletes tracked manifests;
  reproduce.sh hashes the s{seed}/ layouts too

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
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Giorgio Gilestro 2026-09-13 17:00:40 +01:00
parent 84124de143
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paper/pnas/refs/README.md
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# Zotero library for the manuscript's references
`Evolution of sex for AI.ris` — all 80 references from `paper/pnas/main.md`, with metadata
fetched from the publisher of record rather than retyped.
**To import:** Zotero → File → Import… → choose this file → keep "Place imported collections and
items into new collection" ticked. The collection takes its name from the file, so rename the file
first if you want a different folder name.
## How it was built
`build_zotero_library.py` (run from the repo root) parses the numbered reference list, resolves a DOI
for each entry, and fetches authoritative metadata by content negotiation against doi.org, which
serves both Crossref and DataCite records. Each Zotero item carries its manuscript reference number
in the Extra/Notes field, so an item can be traced back to its citation.
- **77 of 80 resolved from a DOI.** 53 DOIs were already printed in the manuscript; the rest were
found by Crossref title search, accepted only when the returned title actually matched (a plain
relevance score is not enough — Crossref answers confidently for pre-DOI works).
- **2 needed a hand-verified DOI:** ref 17 (Brinkmann et al., *Machine culture*), where the search
returned a different paper with a near-identical title, and ref 64 (Schwarz et al., *Progress &
Compress*), a PMLR paper with no Crossref DOI, cited by its arXiv DOI instead.
- **3 genuinely predate DOIs** and are written out by hand in the script: Jenkin 1867, Fisher 1930
(book), Templeton 1986 (book chapter).
`resolution-report.tsv` records the outcome and source for every entry.
`references.csl.json` is the same library as CSL-JSON, for any tool that prefers it.
## Notes on the records
arXiv DOIs come back from DataCite uppercased and with no venue; the script restores the canonical
`10.48550/arXiv.NNNN` casing and sets the publication to *arXiv* with the identifier in the archive
field, so those items do not import as untitled journal articles. Publisher abstracts arrive wrapped
in JATS markup with HTML entities and hard line breaks, all of which are stripped — RIS is
line-oriented, and an unescaped abstract silently corrupts the record that follows it.
Re-run the script after any change to the reference list; it is a pure function of `main.md`.