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/fig2_grounding_sweep/README.md

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+# E2 — A tiny dose of real data rescues diversity (the headline)
+
+**Claim tested:** how much *real* data must you mix back in each generation to stop collapse — a
+lot, or a little?
+
+**Setup (Layer 1, pure math).** `K = 1000` items, Zipf truth `p*`, `n = 200` inherited samples per
+generation, 500 generations, 100 repeats. Each generation we also mix in `m` fresh **real** samples
+drawn from `p*`. The knob swept is the **grounding fraction** `g = m/(n+m)` — the share of the
+training pool that is real — across `g ∈ {0, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.4}`.
+
+### Symbols
+- **`g`** grounding fraction (share of real data); **`g*`** the *critical* value that restores diversity.
+- **`p*`** truth, **`p_t`** model, **`H`** diversity, **`H*`** truth's diversity.
+- **grounding = "immigration"** in the genetics analogy: real samples are migrants that re-introduce alleles drift keeps killing.
+
+### The four panels
+1. **Trajectories.** Diversity `H` over generations, one line per `g` (dark = dry, bright = more
+   grounding). `g = 0` slides toward 0; any `g > 0` levels off on a plateau — the collapse is
+   arrested.
+2. **The phase boundary (the headline).** Dots = stationary diversity vs `g`; the black dashed curve
+   is the *exact* closed-form equilibrium `H_eq`; the red line marks the critical
+   **`g* ≈ 0.048` (95% CI [0.047, 0.050])** where `H` reaches 95% of the truth's diversity. Only
+   **~5% real data** buys back essentially all the diversity. The `g = 0` point is drawn hollow (it
+   is still sliding — its true equilibrium is 0).
+3. **Tail coverage.** Fraction of the rare tail retained, by item-count (red) and truth-mass-weighted
+   (purple). Both rise with `g` but stay modest at feasible grounding: a little grounding restores
+   *diversity* long before it restores the *deep* tail — which motivates E4 (recombination) and E6.
+4. **Per-rarity band.** The tail split into rarity bands (bright = shallowest, dark = deepest). Deep
+   bands lag: an item survives only once `m·p*ᵢ ≳ 1` (enough real samples per generation to land it
+   at least once). The sharp threshold lives here, in discrete item survival — not in the smooth `H`.
+
+### Takeaway
+There is a **critical grounding fraction `g* ≪ 1`**: a small, constant trickle of reality
+indefinitely holds off collapse. **Falsifier (not triggered):** if diversity had only recovered as
+`g → 1`, the practical thesis would die. It recovers at `g ≈ 0.05`.

results/fig2_grounding_sweep/manifest.json

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+{
+  "experiment": "E2_grounding_phase_boundary",
+  "master_seed": 20260704,
+  "git_commit": "a6eb9b75124779375fa1a0b3a64115ecd705b218",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0"
+  },
+  "rows": 400800,
+  "results_sha256": "aa8633171f833611b9c2cde3d13c61e65a81a7c9c6cef5bc76a79127d8af59a3"
+}

results/fig2_grounding_sweep/resolved_config.yaml

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+experiment: E2_grounding_phase_boundary
+seed: 20260704
+n_replicates: 100
+source_config:
+  experiment: E2_grounding_phase_boundary
+  seed: 20260704
+  n_replicates: 100
+  generations: 500
+  truth:
+    K: 1000
+    R: 1
+    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: 0
+      policy: proportional
+    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: g
+    values:
+    - 0.0
+    - 0.005
+    - 0.01
+    - 0.02
+    - 0.05
+    - 0.1
+    - 0.2
+    - 0.4
+  output:
+    dir: results/fig2_grounding_sweep
+grid:
+- label:
+    g: 0.0
+    m: 0
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 0
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.005
+    m: 1
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 1
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.01
+    m: 2
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 2
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.02
+    m: 4
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 4
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.05
+    m: 11
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 11
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.1
+    m: 22
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 22
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.2
+    m: 50
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 50
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    g: 0.4
+    m: 133
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 1
+      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: 133
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 500
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09