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/E7/resolved_config.yaml

@@ -1,23 +0,0 @@
-experiment: E7
-seed: 20260705
-n_replicates: 20
-source_config:
-  experiment: E7
-  kind: genotype_lineage
-  seed: 20260705
-  n_replicates: 20
-  genotype:
-    L: 12
-    n: 150
-    mu: 0.02
-    base: 1.3
-    recomb_rate: 0.0
-    init: wrong
-  generations: 120
-  sweep:
-  - param: genotype.recomb_rate
-    values:
-    - 0.0
-    - 1.0
-  output:
-    dir: results/E7