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/E14.yaml

@@ -1,34 +0,0 @@
-experiment: E14
-kind: mating_system
-seed: 20260709
-n_replicates: 20
-
-# (Mating systems — monogamy vs promiscuity): a finite population of genotypes evolves on a Kauffman
-# NK landscape, recombining sexually, but the MATE-POOL BREADTH is swept. Agents sit on a ring; an
-# offspring's second parent is drawn from a window of half-width ~ breadth*N/2 around the focal parent,
-# and selection is LOCAL (offspring competes only against the incumbent at its ring position). breadth
-# -> 0 is monogamous / structured (local mating, isolation by distance); breadth = 1 is promiscuous /
-# panmictic (mate with anyone). Crossed with ruggedness K, this is the mating-system image of the E9
-# design rule. Expect: on smooth landscapes (K low) promiscuity maximises the best fitness (spread the
-# single good direction fastest); as ruggedness rises the OPTIMAL breadth SHRINKS toward an intermediate
-# value (full promiscuity prematurely converges below it); and diversity + occupied local optima are
-# monotonically destroyed by breadth at every K, most severely on rugged landscapes. Falsifier: the best
-# breadth is independent of K (no crossover), or promiscuity is best at every ruggedness.
-
-mating:
-  L: 12              # loci (genotype space 2^L)
-  N: 48              # population size (ring positions)
-  breadth: 1.0       # mate-pool breadth in [0,1] (overwritten by the sweep)
-  K: 0               # landscape ruggedness / epistasis (overwritten by the sweep)
-  recomb_rate: 0.5   # per-gap crossover rate (near-free reassortment within a mating)
-  mu: 0.003          # per-locus mutation rate
-
-generations: 60
-
-sweep:
-  - param: mating.K
-    values: [0, 3, 6, 10]
-  - param: mating.breadth
-    values: [0.03, 0.08, 0.17, 0.35, 0.6, 1.0]
-
-output: {dir: results/E14}