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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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tasks/lessons.md
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@ -92,7 +92,7 @@ E9, H1"; spell codenames out.
## 2026-09-11 — check the figure panel inventory before flagging cross-references
In the manuscript review I flagged Table 1's "Fig. 4C–E" and "Fig. 3C" as inconsistent with the text. They were
correct: `make_figs.py` puts the E11 ablation in Fig. 4's bottom row and the predictive grid in Fig. 3C–D; the text
simply failed to cite them. Rule: before calling a cross-reference wrong, read `paper/pnas/make_figs.py` and the
simply failed to cite them. Rule: before calling a cross-reference wrong, read `paper/manuscript/make_figs.py` and the
captions in `build.py` for the panel inventory; the fix is usually a missing citation in the text, not a wrong table.
## 2026-09-11 — never type a result number that a script has not printed
@ -103,7 +103,7 @@ print it first. This is the same rule the plan stated ("copied from the stats-sc
typed") and I broke it within the hour.
## Reference numbers hardcoded outside the renumber path (2026-09-11)
`renumber_refs.py` rewrites main.md, si.md and build.py captions, but `make_figs.py` carries a literal "(refs. N, M)" in the fig1a grounding cell, which went stale after references were added. Rule: after any renumber, grep `refs\.` and `ref\.` across `paper/pnas/*.py` and fix by hand (or extend renumber_refs.py to cover make_figs.py). Also: fig text is rendered, so verify by `pdftotext figs/fig1a.pdf`, not by grepping the source alone.
`renumber_refs.py` rewrites main.md, si.md and build.py captions, but `make_figs.py` carries a literal "(refs. N, M)" in the fig1a grounding cell, which went stale after references were added. Rule: after any renumber, grep `refs\.` and `ref\.` across `paper/manuscript/*.py` and fix by hand (or extend renumber_refs.py to cover make_figs.py). Also: fig text is rendered, so verify by `pdftotext figs/fig1a.pdf`, not by grepping the source alone.
## 2026-09-12 — GG's manuscript comments: heralds, undefined terms, and phantom SI references
Forty-five comments on the ODT. Three patterns. (1) **Herald sentences** ("Two boundaries follow.",