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Restructure: descriptive tier and experiment names, paper/manuscript

Browse source 
- 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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results/fig2_mnist_collapse/manifest.json Normal file
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{
"experiment": "mnist_collapse",
"master_seed": 20260705,
"git_commit": "3b9f4f789358a442d510bf2d609aab0986834ac5",
"python": "3.14.5",
"libraries": {
"numpy": "2.5.0",
"scipy": "1.18.0",
"pandas": "3.0.3",
"pyarrow": "24.0.0",
"torch": "2.12.1",
"torchvision": "0.27.1"
},
"rows": 128,
"results_sha256": "d808003e0e01247923996c94eff18c430308448e23bb5d102aa860701145131e",
"layer": "1.5",
"tier": "mnist",
"model_kind": "convvae",
"oracle_ckpt_sha256": "7ff2cc619861daacf8168277c83cde29483554c92d732a24db9fdaa446fa9ff8",
"oracle_mode_accuracy": 0.9847,
"oracle_class_accuracy": 0.9847,
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