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/figS12_quality_diversity/README.md

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+# E5 — Quality-diversity selection preserves diversity where greedy selection destroys it
+
+**Claim tested:** if each generation you *select* which outputs to keep, does chasing the "best"
+outputs (greedy) accelerate collapse — and does rewarding novelty instead prevent it?
+
+**Setup (Layer 1, pure math).** `K = 500` items, Zipf truth, `n = 200`, 400 generations, 100 repeats,
+all arms given the same grounding. Three selection modes: **none** (grounding only, no selection),
+**greedy** (keep the fittest — highest-`p*` — items), and **quality-diversity (QD)** (a novelty
+bonus `w_i ∝ f_i · p_i^{-α}` that up-weights rare items). The novelty exponent `α` is swept over
+`{0.5, 1, 2}`.
+
+### Symbols
+- **greedy** — select toward the fittest/most-probable items (directional pressure).
+- **QD (quality-diversity)** — select for fitness *and* novelty; `α` = strength of the novelty bonus.
+- **`H`** diversity; **support** = number of distinct items surviving.
+
+### The three panels
+1. **Diversity trajectories.** `H` over generations: red = greedy (crashes toward ~0, i.e. fixation
+   on a few items); orange/blue = QD at `α = 1, 2` (holds a high plateau); green = none (reference).
+   Greedy selection is a *second* collapse engine on top of drift.
+2. **Novelty dose–response.** Stationary `H` vs the novelty exponent `α` for QD (orange dots), with
+   greedy (red dashed) and none (green dashed) as reference lines. QD sits above greedy for **every**
+   `α`, and rises as the novelty bonus strengthens.
+3. **Surviving items per arm.** Stationary support (number of distinct items alive) as bars: greedy is
+   lowest; QD arms keep progressively more items alive as `α` grows; none is the reference.
+
+### Takeaway
+Optimising only for "what looks best" (greedy) collapses the population onto a handful of winners; a
+novelty-rewarding, quality-diversity objective actively **re-introduces and holds the tail**. Key
+numbers: greedy `H ≈ 0.01` (near-total fixation) vs QD `H ≈ 0.48–0.88` rising with `α`.
+**Falsifier (not triggered):** if QD's stationary `H` had been ≤ greedy's, quality-diversity would be
+doing no work.

results/figS12_quality_diversity/manifest.json

@@ -0,0 +1,14 @@
+{
+  "experiment": "E5_qd_vs_greedy",
+  "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": 360900,
+  "results_sha256": "16281de4d88951a0688ce8acf82ea9c122034b3faa9be7375b884f46e7b26786"
+}

results/figS12_quality_diversity/resolved_config.yaml

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+experiment: E5_qd_vs_greedy
+seed: 20260704
+n_replicates: 100
+source_config:
+  experiment: E5_qd_vs_greedy
+  seed: 20260704
+  n_replicates: 100
+  generations: 400
+  truth:
+    K: 500
+    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: 10
+      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: dynamics.selection.mode
+    values:
+    - none
+    - greedy
+    - qd
+  - param: dynamics.selection.novelty_alpha
+    values:
+    - 0.5
+    - 1.0
+    - 2.0
+  output:
+    dir: results/figS12_quality_diversity
+grid:
+- label:
+    mode: none
+    novelty_alpha: 0.5
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.5
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: none
+    novelty_alpha: 1.0
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 1.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: none
+    novelty_alpha: 2.0
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 2.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: greedy
+    novelty_alpha: 0.5
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: greedy
+        novelty_alpha: 0.5
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: greedy
+    novelty_alpha: 1.0
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: greedy
+        novelty_alpha: 1.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: greedy
+    novelty_alpha: 2.0
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: greedy
+        novelty_alpha: 2.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: qd
+    novelty_alpha: 0.5
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: qd
+        novelty_alpha: 0.5
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: qd
+    novelty_alpha: 1.0
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: qd
+        novelty_alpha: 1.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    mode: qd
+    novelty_alpha: 2.0
+  lineage_cfg:
+    truth:
+      K: 500
+      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: 10
+        policy: proportional
+      selection:
+        mode: qd
+        novelty_alpha: 2.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09