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/E11.yaml

@@ -1,40 +0,0 @@
-experiment: E11
-kind: dynamic_society
-seed: 20260705
-n_replicates: 12
-
-# (The dynamic Lamarckian society — the vertical claim, C3): a finite population of agents (genotypes)
-# evolves on a rugged NK fitness landscape that IS reality. The full society composes the four
-# operators the whole study built toward — grounding, directed recombination (sex), quality-diversity
-# selection, and mutation — and a 4-arm ablation shows each is load-bearing. Grounding is made load-
-# bearing via the consensus-conformity (self-consumption) mechanism: selection acts on
-# g*true_fitness + (1-g)*conformity, so at g=0 the society optimises agreement with its own majority
-# rather than reality and drifts to a fit-looking but actually-poor consensus. Expect: FULL climbs to
-# near the global optimum while maintaining diversity longest; NO_GROUNDING collapses to the unfit
-# consensus; NO_SEX plateaus (can't recombine to escape local optima); NO_DIVERSITY (greedy) collapses
-# diversity fast and stalls at a worse local optimum. Falsifier: an ablation matches the full society,
-# or the full society fails to exceed every ablation.
-
-society:
-  L: 12
-  K: 8               # landscape ruggedness (epistasis) — rugged enough that diversity + sex matter
-  N: 60              # population size
-  g: 0.85            # grounding fraction (overwritten to 0 in the no_grounding arm)
-  mu: 0.03           # per-locus mutation rate
-  novelty: 0.5       # quality-diversity weight (0 in the no_diversity/greedy arm)
-  n_off: 120         # directed-recombination offspring pool per generation
-  recomb_rate: 0.2   # crossover rate
-  sex: true          # directed recombination on (false in the no_sex arm)
-  select: qd         # quality-diversity survival (greedy in the no_diversity arm)
-
-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/E11}