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/E2.yaml

@@ -1,36 +0,0 @@
-experiment: E2_grounding_phase_boundary
-seed: 20260704
-n_replicates: 100
-generations: 500   # long enough that the g=0 arm slides toward 0 while g>0 arms plateau
-
-# Headline experiment (blueprint 2.5-E2): sweep the grounding fraction g = m/(n+m);
-# single teacher; proportional grounding (Multinomial(m, p*), the immigration model the
-# exact H_eq of 2.4-3 is derived for); no selection. R=1 so the sweep tracks the closed
-# form. Expect a critical g* << 1 above which stationary H and tail mass stabilise at a
-# positive value tracking H_eq = H* * m(2n+m-1)/(n+2nm+m^2), below which they collapse.
-truth:
-  K: 1000
-  R: 1
-  tail: zipf
-  zipf_s: 1.1
-  tail_frac: 0.5
-  tail_threshold: 1.0e-3
-  init: truth
-
-dynamics:
-  n: 200
-  teachers: {K_T: 1, rho: 0.0, q: 1.0}
-  grounding: {m: 0, policy: proportional}   # m is overwritten per g by the sweep
-  selection: {mode: none, novelty_alpha: 0.0}
-  remint: {enabled: false, period: null, H_gate: null}
-
-metrics:
-  kl_floor: 1.0e-9
-  support_eps: 1.0e-9
-
-sweep:
-  - param: g
-    values: [0.0, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.4]
-
-output:
-  dir: results/E2