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/inheritance/figS5_aimed_grounding.yaml

@@ -0,0 +1,40 @@
+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/figS5_aimed_grounding