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.