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/fig4_society_ablation/resolved_config.yaml

@@ -0,0 +1,37 @@
+experiment: E11
+seed: 20260705
+n_replicates: 12
+source_config:
+  experiment: E11
+  kind: dynamic_society
+  seed: 20260705
+  n_replicates: 12
+  society:
+    L: 12
+    K: 8
+    N: 60
+    g: 0.85
+    mu: 0.03
+    novelty: 0.5
+    n_off: 120
+    recomb_rate: 0.2
+    sex: true
+    select: qd
+  generations: 80
+  sweep:
+  - param: arm
+    values:
+    - name: full
+      set: {}
+    - name: no_grounding
+      set:
+        society.g: 0.0
+    - name: no_sex
+      set:
+        society.sex: false
+    - name: no_diversity
+      set:
+        society.select: greedy
+        society.novelty: 0.0
+  output:
+    dir: results/fig4_society_ablation