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

results/figS5_aimed_grounding/resolved_config.yaml

@@ -0,0 +1,111 @@
+experiment: E3_region_matched_grounding
+seed: 20260704
+n_replicates: 100
+source_config:
+  experiment: E3_region_matched_grounding
+  seed: 20260704
+  n_replicates: 100
+  generations: 400
+  truth:
+    K: 1000
+    R: 10
+    tail: zipf
+    zipf_s: 1.1
+    tail_frac: 0.5
+    tail_threshold: 0.001
+    init: truth
+  dynamics:
+    n: 200
+    teachers:
+      K_T: 1
+      rho: 0.0
+      q: 1.0
+    grounding:
+      m: 100
+      policy: uniform
+      exercised:
+      - 0
+    selection:
+      mode: none
+      novelty_alpha: 0.0
+    remint:
+      enabled: false
+      period: null
+      H_gate: null
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: dynamics.grounding.policy
+    values:
+    - uniform
+    - matched
+  output:
+    dir: results/figS5_aimed_grounding
+grid:
+- label:
+    policy: uniform
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 10
+      tail: zipf
+      zipf_s: 1.1
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+    dynamics:
+      n: 200
+      teachers:
+        K_T: 1
+        rho: 0.0
+        q: 1.0
+      grounding:
+        m: 100
+        policy: uniform
+        exercised:
+        - 0
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    policy: matched
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 10
+      tail: zipf
+      zipf_s: 1.1
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+    dynamics:
+      n: 200
+      teachers:
+        K_T: 1
+        rho: 0.0
+        q: 1.0
+      grounding:
+        m: 100
+        policy: matched
+        exercised:
+        - 0
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09