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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
This commit is contained in:
Giorgio Gilestro 2026-09-13 17:00:40 +01:00
parent 84124de143
commit ab3dc10587
240 changed files with 477 additions and 476 deletions
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6
tasks/workorder-pnas-submission.md
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@ -154,7 +154,7 @@ re-run md2tex + tectonic at that point)
## Phase 4 — The PNAS manuscript — Weeks 3–4
- [x] **Restructure** → PNAS research article draft (`paper/pnas/main.md` + build.py + PDF, 2026-08-11:
- [x] **Restructure** → PNAS research article draft (`paper/manuscript/main.md` + build.py + PDF, 2026-08-11:
significance/abstract/intro/Table-1 dictionary/results ladder incl. the predictive test at
second-review calibration/discussion with design rules + ledger + limits/methods; ~5.6k words main).
*(Remaining polish at submission: pnas.cls reflow, numeric refs, bespoke unified figures.)*
@ -177,7 +177,7 @@ re-run md2tex + tectonic at that point)
- [ ] **Dual-audience devices**: Table 1 = the population-genetics ↔ machine-learning dictionary;
every term defined in one clause at first use; keep "the ML statement / the genetics statement"
paired-paragraph device, compressed.
- [x] **Figures: publication-ready** (paper/pnas/make_figs.py re-plots all 6 figures from committed
- [x] **Figures: publication-ready** (paper/manuscript/make_figs.py re-plots all 6 figures from committed
artifacts as unified, lettered, codename-free panels — no suptitles, plain-language labels;
fig1 A-B grounding+MNIST montage (title band cropped), fig2 A-B blending/Fisher-Muller,
fig3 A-D rugged+mating, fig4 A-C society, fig5 A-F speciation x3 tiers, fig6 A-D LLM tier;
@ -186,7 +186,7 @@ re-run md2tex + tectonic at that point)
montage — the one image both audiences get instantly; 3 sex: Fisher–Muller/outbreeding/directed +
merge-don't-average; 4 speciation across three tiers; 5 society ablation + headroom law).
Everything else → SI figures. All regenerated from committed parquet.
- [x] **SI Appendix skeleton** (`paper/pnas/si.md`: propositions, claims ledger, per-tier methods,
- [x] **SI Appendix skeleton** (`paper/manuscript/si.md`: propositions, claims ledger, per-tier methods,
statistics, figure list). Original plan: results-summary.md as the skeleton; full methods, all closed forms +
tolerances, per-experiment configs/seeds, the E13 floor proposition, confusion matrices,
reproduce.sh instructions.