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

figures/plot_figS3_rebaselining.py

@@ -0,0 +1,76 @@
+"""E6 figure: the re-minting gate and irreversibility.
+
+Re-minting freezes the current distribution as the new grounding reference and discards
+the original truth. Re-minting a collapsed lineage locks in the collapse: KL to the
+original truth diverges, because the lost original tails can no longer be grounded.
+Gating re-mint on diversity refuses to re-mint while collapsed and keeps KL bounded;
+re-minting a healthy lineage is harmless. Usage:  python figures/plot_figS3_rebaselining.py [results/figS3_rebaselining]
+"""
+
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+sys.path.insert(0, str(Path(__file__).parent))
+from _figlib import load_bundle, savefig, letter_axes  # noqa: E402
+
+STYLE = {
+    "healthy_remint":     ("#2ca02c", "re-mint while healthy (H high)"),
+    "collapsed_remint":   ("#d62728", "re-mint while collapsed (ungated)"),
+    "collapsed_gated":    ("#1f77b4", "collapsed + diversity gate"),
+    "collapsed_noremint": ("#7f7f7f", "collapsed, no re-mint (baseline)"),
+}
+
+
+def main(results_dir: str = "results/figS3_rebaselining") -> None:
+    df, cfg = load_bundle(results_dir)
+    period = cfg["dynamics"]["remint"]["period"]
+    G = cfg["generations"]
+    remint_gens = list(range(period, G + 1, period))
+
+    fig, axes = plt.subplots(1, 2, figsize=(13, 4.6))
+
+    # Panel 1: forward KL to the ORIGINAL truth
+    ax = axes[0]
+    for arm, (c, lab) in STYLE.items():
+        s = df[df["arm"] == arm].groupby("generation")["forward_kl"]
+        mean, sem = s.mean(), s.sem()
+        ax.plot(mean.index, mean.values, color=c, label=lab)
+        ax.fill_between(mean.index, mean - 1.96 * sem, mean + 1.96 * sem,
+                        color=c, alpha=0.15)
+    for g in remint_gens:
+        ax.axvline(g, ls=":", color="k", lw=0.8, alpha=0.5)
+    ax.set(xlabel="generation", ylabel=r"forward KL to original truth",
+           title="Re-minting while collapsed locks in divergence")
+    ax.legend(frameon=False, fontsize=8)
+
+    # Panel 2: heterozygosity (which arms are collapsed; gate reads this)
+    ax = axes[1]
+    gate = None
+    for arm, (c, lab) in STYLE.items():
+        s = df[df["arm"] == arm].groupby("generation")["heterozygosity"].mean()
+        ax.plot(s.index, s.values, color=c, label=lab)
+    # draw the gate threshold used by the gated arm
+    for v in cfg["sweep"][0]["values"]:
+        if v["name"] == "collapsed_gated":
+            gate = v["set"].get("dynamics.remint.H_gate")
+    if gate is not None:
+        ax.axhline(gate, ls="--", color="k", lw=1)
+        ax.annotate(f"gate H={gate}", (G * 0.02, gate + 0.02), fontsize=8)
+    for g in remint_gens:
+        ax.axvline(g, ls=":", color="k", lw=0.8, alpha=0.5)
+    ax.set(xlabel="generation", ylabel="heterozygosity $H$",
+           title="Diversity at re-mint time (the gate reads this)")
+    ax.legend(frameon=False, fontsize=8)
+
+    fig.tight_layout()
+    letter_axes(fig)
+    savefig(fig, results_dir, "figS3_rebaselining")
+
+
+if __name__ == "__main__":
+    main(*sys.argv[1:])