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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/workorder-llm-society.md
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@ -83,7 +83,7 @@ disagreement), consensus accuracy, conformity−truth gap. E11's three panels re
+0.24 vs +0.16 in `full`. One seed, N=6: direction only. `results/llm_society`.
- [ ] GG gate: review pilot curves before the campaign
- [ ] `hpc/llm_society.pbs` array job (arm × seed) → campaign
- [ ] Figure `paper/pnas/make_figs.py` panel(s); fold into main.md (replaces the "open" cell)
- [ ] Figure `paper/manuscript/make_figs.py` panel(s); fold into main.md (replaces the "open" cell)
- [ ] 7B headline confirm (optional, post-campaign decision)
## Open design decisions (defaults chosen; GG may override)