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/kernel_smooth/resolved_config.yaml

@@ -1,82 +0,0 @@
-experiment: kernel_smooth
-seed: 20260705
-n_replicates: 24
-source_config:
-  experiment: kernel_smooth
-  kind: lineage
-  seed: 20260705
-  n_replicates: 24
-  truth:
-    K: 256
-    R: 1
-    tail: zipf
-    zipf_s: 1.3
-    tail_threshold: 0.001
-    init: truth
-  dynamics:
-    n: 200
-    grounding:
-      m: 0
-      policy: proportional
-    kernel:
-      reset: 0.0
-      temperature: 1.0
-      floor: 0.0
-  generations: 100
-  metrics:
-    kl_floor: 1.0e-09
-    support_eps: 1.0e-09
-  sweep:
-  - param: dynamics.kernel.reset
-    values:
-    - 0.0
-    - 0.006
-  output:
-    dir: results/kernel_smooth
-grid:
-- label:
-    reset: 0.0
-  lineage_cfg:
-    truth:
-      K: 256
-      R: 1
-      tail: zipf
-      zipf_s: 1.3
-      tail_threshold: 0.001
-      init: truth
-    dynamics:
-      n: 200
-      grounding:
-        m: 0
-        policy: proportional
-      kernel:
-        reset: 0.0
-        temperature: 1.0
-        floor: 0.0
-    generations: 100
-    metrics:
-      kl_floor: 1.0e-09
-      support_eps: 1.0e-09
-- label:
-    reset: 0.006
-  lineage_cfg:
-    truth:
-      K: 256
-      R: 1
-      tail: zipf
-      zipf_s: 1.3
-      tail_threshold: 0.001
-      init: truth
-    dynamics:
-      n: 200
-      grounding:
-        m: 0
-        policy: proportional
-      kernel:
-        reset: 0.006
-        temperature: 1.0
-        floor: 0.0
-    generations: 100
-    metrics:
-      kl_floor: 1.0e-09
-      support_eps: 1.0e-09