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/E4.yaml

@@ -1,34 +0,0 @@
-experiment: E4_multiteacher_decorrelation
-kind: coverage
-seed: 20260704
-n_replicates: 200
-
-# Multi-teacher recombination (blueprint 2.5-E4 / 2.7.1). Build K_T teachers with exact
-# marginal retention q and pairwise retention-correlation rho, form the pupil from their
-# mixture (n draws total = matched budget), and report TWO coverages:
-#   union_coverage    -> construction-level U(K_T,rho,q) (must match the closed form)
-#   surviving_coverage-> tail items that survive the pupil's size-n resampling (+ grounding)
-# Expect: both rise with K_T and (1-rho); at rho=1 many teachers give no benefit over one;
-# the union-surviving gap shrinks as grounding g rises.
-truth:
-  K: 500
-  R: 1
-  tail: zipf
-  zipf_s: 1.1
-  tail_frac: 0.5
-  tail_threshold: 2.0e-3
-
-coverage:
-  n: 300          # pupil sample size (matched budget across teachers)
-  q: 0.5          # per-teacher marginal tail retention
-
-sweep:
-  - param: K_T
-    values: [1, 2, 3, 5]
-  - param: rho
-    values: [0.0, 0.25, 0.5, 0.75, 1.0]
-  - param: g
-    values: [0.0, 0.02, 0.05]
-
-output:
-  dir: results/E4