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Giorgio Gilestro ab3dc10587 Restructure: descriptive tier and experiment names, paper/manuscript 
- 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
2026-09-13 17:00:40 +01:00
..
_figlib.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
mnist_montage.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_bridge.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_collapse.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_collapse_null.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_curriculum_cull.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_curriculum_timing.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_fig2_grounding_sweep.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_fig2_mnist_collapse.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_fig4_society_ablation.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_fig5_speciation_bdm.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS1_architectures.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS3_rebaselining.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS5_aimed_grounding.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS6_grounding_rnn.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS8_multiparent_union.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS9_specialist_superparent.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS10_rugged_landscapes.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS11_directed_recombination.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS12_quality_diversity.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_figS13_mating_breadth.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_kernel.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_llm_compose.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_directed.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_epistasis.py second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
plot_llm_merge.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_moe.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_seeds.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_smol.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_society.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
plot_llm_speciation.py second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
plot_recombination.py neural: grounding refinement + all five Layer-1.5 figures 2026-07-05 08:14:19 +01:00
plot_sexual_vs_asexual_lineage.py Restructure: descriptive tier and experiment names, paper/manuscript 2026-09-13 17:00:40 +01:00
plot_speciation_real.py E13b/c: harden real-weight speciation — full symmetry group + emergent-divergence null 2026-09-06 12:35:14 +01:00
stats_llm_7b_seeds.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
stats_llm_compose.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
stats_llm_curriculum.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
stats_llm_epistasis.py third review round: mathematical corrections + operator separation + headline calibration 2026-09-06 19:29:09 +01:00
stats_llm_smol.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
stats_llm_society.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00
stats_llm_speciation_seeds.py Manuscript revision and pending experiment work, snapshot before restructuring 2026-09-13 16:54:09 +01:00