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/figS3_rebaselining/README.md

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+# E6 — Re-minting is irreversible; gate it on diversity
+
+**Claim tested:** what happens if you "re-baseline" — declare the current model's output to be the new
+ground truth and throw away the original? If you do this while the model is already collapsed, is the
+damage permanent? And can a simple safeguard prevent it?
+
+**Setup (Layer 1, pure math).** `K = 500`, `n = 200`, 400 generations, 100 repeats. **Re-minting**
+periodically freezes the current distribution as the new grounding reference and *discards the
+original truth* (it survives only as a yardstick for measuring drift). Four arms:
+- **healthy re-mint** — generous grounding (`m = 60`), re-mint while still diverse;
+- **collapsed re-mint (ungated)** — starved grounding (`m = 1`), re-mint anyway;
+- **collapsed + diversity gate** — same starvation, but only re-mint if diversity `H ≥ 0.75`;
+- **collapsed, no re-mint** — the baseline.
+
+### Symbols
+- **re-mint** — adopt the current model's output as the new "reality" and discard the original truth (a founder event).
+- **diversity gate** — refuse to re-mint while `H` is below a threshold (here 0.75).
+- **forward-KL to ORIGINAL truth** — how far the lineage has drifted from the *real* original, even after it changed its own reference.
+
+### The two panels
+1. **Lock-in.** Forward-KL to the *original* truth over generations; dotted verticals mark re-mint
+   events. Red (collapsed, ungated) **jumps up at each re-mint and never comes back** — once the
+   original tails are gone, re-baselining onto the impoverished distribution makes the loss permanent
+   (they can no longer be grounded back). Green (healthy) and blue (gated) stay low; grey (baseline)
+   is the reference.
+2. **What the gate reads.** Diversity `H` over generations, same colour key, with the gate threshold
+   (`H = 0.75`, dashed). The gated arm simply **refuses to re-mint while below the line**, so it never
+   locks in a collapsed state; the ungated collapsed arm re-mints into the floor.
+
+### Takeaway
+Re-minting a collapsed model **crystallises** the collapse — it is a one-way door. A trivial
+safeguard (only re-baseline when diversity is still high) preserves recoverability; re-minting a
+healthy model is harmless. **Falsifier (not triggered):** if the collapsed lineage had recovered its
+original tails after re-minting, the irreversibility claim would be overstated.

results/figS3_rebaselining/manifest.json

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+{
+  "experiment": "E6_remint_gate",
+  "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": 160400,
+  "results_sha256": "083106777ae2f8c5aff47f23a27fa111891c183464ebfee8d015dfc096974a80"
+}

results/figS3_rebaselining/resolved_config.yaml

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+experiment: E6_remint_gate
+seed: 20260704
+n_replicates: 100
+source_config:
+  experiment: E6_remint_gate
+  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: 3
+      policy: proportional
+    selection:
+      mode: none
+      novelty_alpha: 0.0
+    remint:
+      enabled: false
+      period: 150
+      H_gate: null
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: arm
+    values:
+    - name: healthy_remint
+      set:
+        dynamics.grounding.m: 60
+        dynamics.remint.enabled: true
+        dynamics.remint.H_gate: null
+    - name: collapsed_remint
+      set:
+        dynamics.grounding.m: 1
+        dynamics.remint.enabled: true
+        dynamics.remint.H_gate: null
+    - name: collapsed_gated
+      set:
+        dynamics.grounding.m: 1
+        dynamics.remint.enabled: true
+        dynamics.remint.H_gate: 0.75
+    - name: collapsed_noremint
+      set:
+        dynamics.grounding.m: 1
+        dynamics.remint.enabled: false
+  output:
+    dir: results/figS3_rebaselining
+grid:
+- label:
+    arm: healthy_remint
+  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: 60
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: true
+        period: 150
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    arm: collapsed_remint
+  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: 1
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: true
+        period: 150
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    arm: collapsed_gated
+  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: 1
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: true
+        period: 150
+        H_gate: 0.75
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    arm: collapsed_noremint
+  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: 1
+        policy: proportional
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: 150
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09