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/fig5_speciation_bdm/resolved_config.yaml

@@ -0,0 +1,33 @@
+experiment: E12
+seed: 12
+n_replicates: 15
+source_config:
+  experiment: E12
+  kind: speciation
+  seed: 12
+  n_replicates: 15
+  speciation:
+    landscape: bdm
+    L: 20
+    rho:
+    - 0.1
+    - 0.25
+    - 0.5
+    divergences:
+    - 0
+    - 2
+    - 4
+    - 6
+    - 8
+    - 10
+    - 12
+    - 14
+    - 16
+    - 18
+    - 20
+    s: 1.0
+    beta: 1.0
+    recomb_rate: 0.5
+    n_offspring: 500
+  output:
+    dir: results/fig5_speciation_bdm