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_mnist.py

@@ -1,79 +0,0 @@
-"""`mnist_collapse` figure — collapse and grounding-rescue on REAL MNIST images.
-
-External validity for the neural tier: a convolutional VAE retrained each generation on its own
-generated digits collapses — rare (class, thickness) modes die, forward-KL to the Zipf truth
-climbs, support shrinks — while a grounded arm (a fraction of fresh real MNIST images each
-generation) holds the tail. Modes are read by a frozen CNN oracle whose mode accuracy (the
-measurement-noise floor) is annotated from the run manifest. Signs, not magnitudes.
-
-Four panels, dry (g=0) vs grounded, mean ± 95% CI across replicates: (A) forward-KL trajectories;
-(B) support size (distinct modes alive); (C) tail truth-mass alive; (D) heterozygosity. Reads the
-committed bundle (parquet) + manifest.json only.
-
-Usage:  python figures/plot_mnist.py [results/mnist_collapse]
-"""
-
-from __future__ import annotations
-
-import json
-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
-
-sys.path.insert(0, str(Path(__file__).parents[1] / "src"))
-from knowledge.metrics import heterozygosity  # noqa: E402
-from neural.config import MnistCfg  # noqa: E402
-from neural.mnist_data import make_mnist_truth  # noqa: E402
-
-
-def _traj(df, g, col):
-    """Return (generations, mean, 95% half-width) of ``col`` for arm ``g`` across replicates."""
-    sub = df[df["g"] == g]
-    grp = sub.groupby("generation")[col]
-    gens = np.array(sorted(sub["generation"].unique()))
-    return gens, grp.mean().to_numpy(), 1.96 * grp.sem().to_numpy()
-
-
-def main(results_dir: str = "results/mnist_collapse") -> None:
-    df, cfg = load_bundle(results_dir)
-    syn = MnistCfg(**cfg["mnist"])
-    H_star = heterozygosity(make_mnist_truth(syn).p_star)
-    manifest = json.loads((Path(results_dir) / "manifest.json").read_text())
-    oracle_acc = manifest.get("oracle_mode_accuracy", float("nan"))
-
-    g_dry, g_wet = min(df["g"].unique()), max(df["g"].unique())
-    arms = [(g_dry, "#d62728", f"no real data (g={g_dry:g})"), (g_wet, "#2ca02c", f"grounded (g={g_wet:g})")]
-
-    fig, axes = plt.subplots(2, 2, figsize=(13, 9))
-
-    def panel(ax, col, title, ylabel, hline=None):
-        for g, c, lab in arms:
-            gens, m, ci = _traj(df, g, col)
-            ax.plot(gens, m, "-o", color=c, ms=3, label=lab)
-            ax.fill_between(gens, m - ci, m + ci, color=c, alpha=0.2)
-        if hline is not None:
-            ax.axhline(hline[0], ls=":", color="gray", lw=1, label=hline[1])
-        ax.set(xlabel="generation", ylabel=ylabel, title=title)
-        ax.legend(frameon=False, fontsize=9)
-
-    panel(axes[0, 0], "forward_kl", "Without real data forward-KL climbs; grounding holds it",
-          r"forward-KL $D(p^*\Vert\hat p)$")
-    panel(axes[0, 1], "support_size", f"Support collapses (of K={syn.K} modes)",
-          "distinct modes alive", hline=(syn.K, f"$K$={syn.K}"))
-    panel(axes[1, 0], "tail_truth_mass_alive", "Rare tail dies without real data, held by grounding",
-          "tail truth-mass alive")
-    panel(axes[1, 1], "heterozygosity", "Diversity collapses without real data, held by grounding",
-          "heterozygosity $H$", hline=(H_star, "$H^*$"))
-
-    fig.tight_layout()
-    letter_axes(fig)
-    savefig(fig, results_dir, "mnist_collapse")
-
-
-if __name__ == "__main__":
-    main(*sys.argv[1:])