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/figS2_kernel_sharpen/resolved_config.yaml

@@ -0,0 +1,82 @@
+experiment: kernel_sharpen
+seed: 20260705
+n_replicates: 24
+source_config:
+  experiment: kernel_sharpen
+  kind: lineage
+  seed: 20260705
+  n_replicates: 24
+  truth:
+    K: 30
+    R: 1
+    tail: zipf
+    zipf_s: 1.5
+    tail_threshold: 0.01
+    init: truth
+  dynamics:
+    n: 6000
+    grounding:
+      m: 0
+      policy: proportional
+    kernel:
+      reset: 0.0
+      temperature: 1.0
+      floor: 0.0
+  generations: 15
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: dynamics.kernel.temperature
+    values:
+    - 1.0
+    - 0.8
+  output:
+    dir: results/figS2_kernel_sharpen
+grid:
+- label:
+    temperature: 1.0
+  lineage_cfg:
+    truth:
+      K: 30
+      R: 1
+      tail: zipf
+      zipf_s: 1.5
+      tail_threshold: 0.01
+      init: truth
+    dynamics:
+      n: 6000
+      grounding:
+        m: 0
+        policy: proportional
+      kernel:
+        reset: 0.0
+        temperature: 1.0
+        floor: 0.0
+    generations: 15
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    temperature: 0.8
+  lineage_cfg:
+    truth:
+      K: 30
+      R: 1
+      tail: zipf
+      zipf_s: 1.5
+      tail_threshold: 0.01
+      init: truth
+    dynamics:
+      n: 6000
+      grounding:
+        m: 0
+        policy: proportional
+      kernel:
+        reset: 0.0
+        temperature: 0.8
+        floor: 0.0
+    generations: 15
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09