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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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4
figures/plot_bridge.py
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@ -24,8 +24,8 @@ sys.path.insert(0, str(Path(__file__).parent))
from _figlib import load_bundle, mean_ci, savefig # noqa: E402
sys.path.insert(0, str(Path(__file__).parents[1] / "src"))
from knowledge.analysis import critical_grounding, reduce_to_stationary # noqa: E402
from knowledge.metrics import heterozygosity # noqa: E402
from inheritance.analysis import critical_grounding, reduce_to_stationary # noqa: E402
from inheritance.metrics import heterozygosity # noqa: E402
from neural.config import SyntheticCfg # noqa: E402
from neural.synthetic import make_mode_truth # noqa: E402