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

results/collapse_null/resolved_config.yaml

@@ -34,7 +34,7 @@ source_config:
     kl_floor: 1.0e-09
     support_eps: 1.0e-09
   output:
-    dir: results/E1
+    dir: results/collapse_null
 grid:
 - label: {}
   lineage_cfg:

results/fig2_grounding_sweep/resolved_config.yaml

@@ -45,7 +45,7 @@ source_config:
     - 0.2
     - 0.4
   output:
-    dir: results/E2
+    dir: results/fig2_grounding_sweep
 grid:
 - label:
     g: 0.0

results/fig2_mnist_collapse/resolved_config.yaml

@@ -44,7 +44,7 @@ source_config:
     - 0.0
     - 0.1
   output:
-    dir: results/mnist_collapse
+    dir: results/fig2_mnist_collapse
 grid:
 - label:
     g: 0.0

results/fig4_society_ablation/resolved_config.yaml

@@ -34,4 +34,4 @@ source_config:
         society.select: greedy
         society.novelty: 0.0
   output:
-    dir: results/E11
+    dir: results/fig4_society_ablation

results/fig5_speciation_bdm/README.md

@@ -11,11 +11,11 @@ capability landscape.
 
 **Setup.** Pure seeded NumPy on the E7–E11 genotype machinery (bitwise-reproducible; no external
 simulator, whose separate RNG would break that guarantee). Two landscapes:
-- **BDM** (`configs/layer1/E12.yaml`, headline): an ancestor; two lineages each substitute a *disjoint*
+- **BDM** (`configs/inheritance/fig5_speciation_bdm.yaml`, headline): an ancestor; two lineages each substitute a *disjoint*
   set of loci (each parent adaptive, neither carrying an incompatibility); a fraction `ρ` of
   cross-lineage locus pairs are BDMIs (penalty `s`), biting only when a hybrid inherits *both* derived
   alleles. Sweep divergence `d` (substitutions) for several `ρ`; `L=20`, 15 reps.
-- **NK** (`configs/layer1/E12_nk.yaml`): parents are *local optima* (hill-climbed) on a Kauffman NK
+- **NK** (`configs/inheritance/speciation_bdm_nk.yaml`): parents are *local optima* (hill-climbed) on a Kauffman NK
   landscape; sweep ruggedness `K`. The emergent version.
 
 ### Results

results/fig5_speciation_bdm/resolved_config.yaml

@@ -30,4 +30,4 @@ source_config:
     recomb_rate: 0.5
     n_offspring: 500
   output:
-    dir: results/E12
+    dir: results/fig5_speciation_bdm

results/figS10_rugged_landscapes/resolved_config.yaml

@@ -27,4 +27,4 @@ source_config:
     - 0.35
     - 0.5
   output:
-    dir: results/E9
+    dir: results/figS10_rugged_landscapes

results/figS11_directed_recombination/resolved_config.yaml

@@ -22,4 +22,4 @@ source_config:
     - 8
     - 10
   output:
-    dir: results/E10
+    dir: results/figS11_directed_recombination

results/figS12_quality_diversity/resolved_config.yaml

@@ -45,7 +45,7 @@ source_config:
     - 1.0
     - 2.0
   output:
-    dir: results/E5
+    dir: results/figS12_quality_diversity
 grid:
 - label:
     mode: none

results/figS13_mating_breadth/resolved_config.yaml

@@ -30,4 +30,4 @@ source_config:
     - 0.6
     - 1.0
   output:
-    dir: results/E14
+    dir: results/figS13_mating_breadth

results/figS1_architectures/resolved_config.yaml

@@ -49,7 +49,7 @@ source_config:
     - 0.0
     - 0.05
   output:
-    dir: results/architectures
+    dir: results/figS1_architectures
 grid:
 - label:
     kind: histogram

results/figS2_kernel_sharpen/README.md

@@ -1,6 +1,6 @@
 # kernel — the learning kernel: why real learners deviate from neutral drift
 
-*(This legend covers both `results/kernel_sharpen/` and `results/kernel_smooth/`; the figure
+*(This legend covers both `results/figS2_kernel_sharpen/` and `results/figS2_kernel_smooth/`; the figure
 `kernel.png` is written into both.)*
 
 **Claim tested.** Neutral Wright–Fisher drift (the histogram bridge, and the baseline of Riis

results/figS2_kernel_sharpen/resolved_config.yaml

@@ -32,7 +32,7 @@ source_config:
     - 1.0
     - 0.8
   output:
-    dir: results/kernel_sharpen
+    dir: results/figS2_kernel_sharpen
 grid:
 - label:
     temperature: 1.0

results/figS2_kernel_smooth/README.md

@@ -1,6 +1,6 @@
 # kernel — the learning kernel: why real learners deviate from neutral drift
 
-*(This legend covers both `results/kernel_sharpen/` and `results/kernel_smooth/`; the figure
+*(This legend covers both `results/figS2_kernel_sharpen/` and `results/figS2_kernel_smooth/`; the figure
 `kernel.png` is written into both.)*
 
 **Claim tested.** Neutral Wright–Fisher drift (the histogram bridge, and the baseline of Riis

results/figS2_kernel_smooth/resolved_config.yaml

@@ -32,7 +32,7 @@ source_config:
     - 0.0
     - 0.006
   output:
-    dir: results/kernel_smooth
+    dir: results/figS2_kernel_smooth
 grid:
 - label:
     reset: 0.0

results/figS3_rebaselining/resolved_config.yaml

@@ -56,7 +56,7 @@ source_config:
         dynamics.grounding.m: 1
         dynamics.remint.enabled: false
   output:
-    dir: results/E6
+    dir: results/figS3_rebaselining
 grid:
 - label:
     arm: healthy_remint

results/figS5_aimed_grounding/resolved_config.yaml

@@ -41,7 +41,7 @@ source_config:
     - uniform
     - matched
   output:
-    dir: results/E3
+    dir: results/figS5_aimed_grounding
 grid:
 - label:
     policy: uniform

results/figS6_grounding_rnn/resolved_config.yaml

@@ -51,7 +51,7 @@ source_config:
     - 0.1
     - 0.2
   output:
-    dir: results/grounding
+    dir: results/figS6_grounding_rnn
 grid:
 - label:
     g: 0.0

results/figS8_multiparent_union/resolved_config.yaml

@@ -36,4 +36,4 @@ source_config:
     - 0.02
     - 0.05
   output:
-    dir: results/E4
+    dir: results/figS8_multiparent_union

results/figS9_specialist_superparent/resolved_config.yaml

@@ -26,4 +26,4 @@ source_config:
     - 0.5
     - 1.0
   output:
-    dir: results/E8
+    dir: results/figS9_specialist_superparent

results/sexual_vs_asexual_lineage/resolved_config.yaml

@@ -20,4 +20,4 @@ source_config:
     - 0.0
     - 1.0
   output:
-    dir: results/E7
+    dir: results/sexual_vs_asexual_lineage

results/speciation_bdm_nk/resolved_config.yaml

@@ -20,4 +20,4 @@ source_config:
     recomb_rate: 0.5
     n_offspring: 200
   output:
-    dir: results/E12_nk
+    dir: results/speciation_bdm_nk