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 · 2026-09-13 17:00:40 +01:00 · ab3dc10587
commit ab3dc10587
parent 84124de143
240 changed files with 477 additions and 476 deletions
--- a/paper/manuscript/figs/si/s10_figS10_rugged_landscapes.pdf
+++ b/paper/manuscript/figs/si/s10_figS10_rugged_landscapes.pdf
--- a/paper/manuscript/figs/si/s11_figS11_directed_recombination.pdf
+++ b/paper/manuscript/figs/si/s11_figS11_directed_recombination.pdf
--- a/paper/manuscript/figs/si/s12_figS12_quality_diversity.pdf
+++ b/paper/manuscript/figs/si/s12_figS12_quality_diversity.pdf
--- a/paper/manuscript/figs/si/s13_figS13_mating_breadth.pdf
+++ b/paper/manuscript/figs/si/s13_figS13_mating_breadth.pdf
--- a/paper/manuscript/figs/si/s14_curriculum_timing.pdf
+++ b/paper/manuscript/figs/si/s14_curriculum_timing.pdf
--- a/paper/manuscript/figs/si/s15_curriculum_cull.pdf
+++ b/paper/manuscript/figs/si/s15_curriculum_cull.pdf
--- a/paper/manuscript/figs/si/s16_llm_smol.pdf
+++ b/paper/manuscript/figs/si/s16_llm_smol.pdf
--- a/paper/manuscript/figs/si/s1_figS1_architectures.pdf
+++ b/paper/manuscript/figs/si/s1_figS1_architectures.pdf
--- a/paper/manuscript/figs/si/s2_kernel.pdf
+++ b/paper/manuscript/figs/si/s2_kernel.pdf
--- a/paper/manuscript/figs/si/s3_figS3_rebaselining.pdf
+++ b/paper/manuscript/figs/si/s3_figS3_rebaselining.pdf
--- a/paper/manuscript/figs/si/s4_fig2_grounding_sweep.pdf
+++ b/paper/manuscript/figs/si/s4_fig2_grounding_sweep.pdf
--- a/paper/manuscript/figs/si/s5_figS5_aimed_grounding.pdf
+++ b/paper/manuscript/figs/si/s5_figS5_aimed_grounding.pdf
--- a/paper/manuscript/figs/si/s6_figS6_grounding_rnn.pdf
+++ b/paper/manuscript/figs/si/s6_figS6_grounding_rnn.pdf
--- a/paper/manuscript/figs/si/s7_fig2_mnist_collapse.pdf
+++ b/paper/manuscript/figs/si/s7_fig2_mnist_collapse.pdf
--- a/paper/manuscript/figs/si/s8_figS8_multiparent_union.pdf
+++ b/paper/manuscript/figs/si/s8_figS8_multiparent_union.pdf
--- a/paper/manuscript/figs/si/s9_figS9_specialist_superparent.pdf
+++ b/paper/manuscript/figs/si/s9_figS9_specialist_superparent.pdf