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/mnist_collapse/resolved_config.yaml

@@ -1,110 +0,0 @@
-experiment: mnist_collapse
-seed: 20260705
-n_replicates: 4
-source_config:
-  experiment: mnist_collapse
-  kind: mnist_lineage
-  seed: 20260705
-  n_replicates: 4
-  mnist:
-    K: 30
-    n_classes: 10
-    style_bins: 3
-    R: 1
-    tail: zipf
-    zipf_s: 1.5
-    tail_threshold: 0.01
-    init: truth
-    data_root: data
-  model:
-    kind: convvae
-    latent: 32
-    epochs: 30
-    lr: 0.001
-    batch_size: 256
-    beta: 1.0
-    n_eval: 10000
-  oracle:
-    epochs: 5
-    lr: 0.001
-    batch_size: 256
-    cache: models/mnist_cnn.pt
-  dynamics:
-    n: 6000
-    grounding:
-      m: 0
-      policy: proportional
-  generations: 15
-  metrics:
-    kl_floor: 1.0e-09
-    support_eps: 1.0e-09
-  sweep:
-  - param: g
-    values:
-    - 0.0
-    - 0.1
-  output:
-    dir: results/mnist_collapse
-grid:
-- label:
-    g: 0.0
-    m: 0
-  lineage_cfg:
-    mnist:
-      K: 30
-      n_classes: 10
-      style_bins: 3
-      R: 1
-      tail: zipf
-      zipf_s: 1.5
-      tail_threshold: 0.01
-      init: truth
-      data_root: data
-    model:
-      kind: convvae
-      latent: 32
-      epochs: 30
-      lr: 0.001
-      batch_size: 256
-      beta: 1.0
-      n_eval: 10000
-    dynamics:
-      n: 6000
-      grounding:
-        m: 0
-        policy: proportional
-    generations: 15
-    metrics:
-      kl_floor: 1.0e-09
-      support_eps: 1.0e-09
-- label:
-    g: 0.1
-    m: 667
-  lineage_cfg:
-    mnist:
-      K: 30
-      n_classes: 10
-      style_bins: 3
-      R: 1
-      tail: zipf
-      zipf_s: 1.5
-      tail_threshold: 0.01
-      init: truth
-      data_root: data
-    model:
-      kind: convvae
-      latent: 32
-      epochs: 30
-      lr: 0.001
-      batch_size: 256
-      beta: 1.0
-      n_eval: 10000
-    dynamics:
-      n: 6000
-      grounding:
-        m: 667
-        policy: proportional
-    generations: 15
-    metrics:
-      kl_floor: 1.0e-09
-      support_eps: 1.0e-09