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

configs/layer1/E12_nk.yaml

@@ -1,22 +0,0 @@
-experiment: E12_nk
-kind: speciation
-seed: 12
-n_replicates: 15
-
-# E12 (NK variant) — the EPISTASIS WEDGE, the paper's distinct falsifiable claim: at matched divergence,
-# mergeability is governed by the EPISTASIS (ruggedness K) of the capability landscape, not by divergence
-# alone (every existing ML merge predictor is a divergence measure). Parents are LOCAL OPTIMA reached by
-# hill-climbing a Kauffman NK landscape from random starts; recombining them exposes broken co-adapted
-# blocks. As K rises, recombining two adapted parents flips from a gain (offspring above the worse parent)
-# to outbreeding depression (offspring below it). K=0 (additive) is the no-isolation control.
-
-speciation:
-  landscape: nk
-  L: 16
-  K: [0, 2, 4, 6, 8, 10]      # ruggedness / epistasis knob
-  n_pairs: 40                 # random parent-pairs (local optima) aggregated per landscape
-  recomb_rate: 0.5
-  n_offspring: 200
-
-output:
-  dir: results/E12_nk