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/figS3_rebaselining.yaml

@@ -0,0 +1,46 @@
+experiment: E6_remint_gate
+seed: 20260704
+n_replicates: 100
+generations: 400
+
+# Re-minting gate / irreversibility (blueprint 2.5-E6). Re-minting freezes the current
+# distribution as the new grounding reference and DISCARDS the original truth. Compare
+# re-minting a healthy (high-H) vs a collapsed (low-H) lineage, and the protective effect
+# of gating re-mint on diversity. Metric: forward KL to the ORIGINAL truth. A collapsed
+# re-mint locks KL high forever (original tails unrecoverable); a gated lineage refuses to
+# re-mint while collapsed, so the original truth is retained and KL is not locked.
+truth:
+  K: 500
+  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: 3, policy: proportional}
+  selection: {mode: none, novelty_alpha: 0.0}
+  remint: {enabled: false, period: 150, H_gate: null}
+
+metrics:
+  kl_floor: 1.0e-9
+  support_eps: 1.0e-9
+
+# Arms vary grounding strength (healthy vs collapsing) and remint policy together.
+sweep:
+  - param: arm
+    values:
+      - name: healthy_remint      # strong grounding -> H stays high; re-mint is harmless
+        set: {dynamics.grounding.m: 60, dynamics.remint.enabled: true, dynamics.remint.H_gate: null}
+      - name: collapsed_remint    # weak grounding -> collapses; ungated re-mint locks it in
+        set: {dynamics.grounding.m: 1, dynamics.remint.enabled: true, dynamics.remint.H_gate: null}
+      - name: collapsed_gated     # weak grounding; gate (0.75) blocks re-mint while H is low
+        set: {dynamics.grounding.m: 1, dynamics.remint.enabled: true, dynamics.remint.H_gate: 0.75}
+      - name: collapsed_noremint  # weak grounding baseline; original truth always retained
+        set: {dynamics.grounding.m: 1, dynamics.remint.enabled: false}
+
+output:
+  dir: results/figS3_rebaselining