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/E3.yaml

@@ -1,40 +0,0 @@
-experiment: E3_region_matched_grounding
-seed: 20260704
-n_replicates: 100
-generations: 400
-
-# Region-matched grounding (blueprint 2.5-E3). Fixed total budget m; the lineage this
-# passage exercises region 0 (the target, carrying its own rare tail). Compare:
-#   uniform  -> spread m evenly over all R regions (region 0 gets only m/R)
-#   matched  -> allocate m to the exercised region(s) only (region 0 gets all of m)
-# Prediction: under uniform, region 0's tail collapses even though global grounding is
-# nonzero; under matched, it persists. Metric: per-region tail-item survival.
-truth:
-  K: 1000
-  R: 10                # 100 items/region; each region an identical Zipf block
-  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: 100             # same total for both arms; uniform => 10/region, matched => 100 to region 0
-    policy: uniform    # overwritten by the sweep
-    exercised: [0]     # region 0 is exercised this passage (matched targets it)
-  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: dynamics.grounding.policy
-    values: [uniform, matched]
-
-output:
-  dir: results/E3