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/figS6_grounding_rnn/resolved_config.yaml

@@ -0,0 +1,379 @@
+experiment: grounding_phase_boundary
+seed: 20260704
+n_replicates: 18
+source_config:
+  experiment: grounding_phase_boundary
+  kind: gen_lineage
+  seed: 20260704
+  n_replicates: 18
+  generations: 30
+  synthetic:
+    K: 256
+    R: 1
+    tail: zipf
+    zipf_s: 1.3
+    tail_frac: 0.5
+    tail_threshold: 0.001
+    init: truth
+    style_len: 3
+    style_vocab: 5
+    id_base: 2
+  model:
+    kind: rnn
+    hidden: 128
+    embed: 24
+    epochs: 25
+    lr: 0.002
+    batch_size: 256
+    n_eval: 15000
+  dynamics:
+    n: 200
+    grounding:
+      m: 0
+      policy: proportional
+    remint:
+      enabled: false
+      period: null
+      H_gate: null
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: g
+    values:
+    - 0.0
+    - 0.005
+    - 0.01
+    - 0.02
+    - 0.035
+    - 0.05
+    - 0.075
+    - 0.1
+    - 0.2
+  output:
+    dir: results/figS6_grounding_rnn
+grid:
+- label:
+    g: 0.0
+    m: 0
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 0
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.005
+    m: 1
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 1
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.01
+    m: 2
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 2
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.02
+    m: 4
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 4
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.035
+    m: 7
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 7
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.05
+    m: 11
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 11
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.075
+    m: 16
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 16
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.1
+    m: 22
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 22
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.2
+    m: 50
+  neural_cfg:
+    synthetic:
+      K: 256
+      R: 1
+      tail: zipf
+      zipf_s: 1.3
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+      style_len: 3
+      style_vocab: 5
+      id_base: 2
+    model:
+      kind: rnn
+      hidden: 128
+      embed: 24
+      epochs: 25
+      lr: 0.002
+      batch_size: 256
+      n_eval: 15000
+    dynamics:
+      n: 200
+      grounding:
+        m: 50
+        policy: proportional
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 30
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09