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_E1.py

@@ -1,64 +0,0 @@
-"""E1 figure: reproduce collapse (null model).
-
-Shows tail-first collapse under pure neutral drift: geometric H decay matching the
-analytic law, tail items dying faster than head items, support -> 1 and forward-KL
-diverging. Usage:  python figures/plot_E1.py [results/E1]
-"""
-
-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, mean_ci, savefig  # noqa: E402
-
-
-def main(results_dir: str = "results/E1") -> None:
-    df, cfg = load_bundle(results_dir)
-    n = cfg["dynamics"]["n"]
-
-    gens, Hmean, Hci = mean_ci(df, "generation", "heterozygosity")
-    H0 = Hmean[0]
-    analytic = H0 * (1.0 - 1.0 / n) ** gens
-
-    m = df.groupby("generation").mean(numeric_only=True)
-
-    fig, axes = plt.subplots(1, 3, figsize=(15, 4.2))
-
-    # Panel 1: heterozygosity decay vs the analytic law
-    ax = axes[0]
-    ax.plot(gens, Hmean, color="#1f77b4", label="simulation (mean)")
-    ax.fill_between(gens, Hmean - Hci, Hmean + Hci, color="#1f77b4", alpha=0.25)
-    ax.plot(gens, analytic, "k--", label=r"$H_0(1-1/n)^t$")
-    ax.set(xlabel="generation", ylabel="heterozygosity $H$",
-           title=f"Geometric decay (n={n})")
-    ax.legend(frameon=False)
-
-    # Panel 2: tail-first — fraction of tail vs head items still alive
-    ax = axes[1]
-    ax.plot(m.index, m["tail_frac_alive"], color="#d62728", label="tail items alive")
-    ax.plot(m.index, m["head_frac_alive"], color="#2ca02c", label="head items alive")
-    ax.set(xlabel="generation", ylabel="fraction of items surviving",
-           title="Tail dies first", yscale="log")
-    ax.legend(frameon=False)
-
-    # Panel 3: support collapse and KL divergence
-    ax = axes[2]
-    ax.plot(m.index, m["support_size"], color="#9467bd", label="support size")
-    ax.set(xlabel="generation", ylabel="support size", yscale="log", title="Collapse")
-    ax2 = ax.twinx()
-    ax2.plot(m.index, m["forward_kl"], color="#ff7f0e", label="forward KL")
-    ax2.set_ylabel(r"forward KL $D_{KL}(p^*\,\|\,p_t)$", color="#ff7f0e")
-    ax.legend(loc="center right", frameon=False)
-
-    fig.suptitle("E1 — distillation without grounding collapses, tail first", y=1.02)
-    fig.tight_layout()
-    savefig(fig, results_dir, "E1")
-
-
-if __name__ == "__main__":
-    main(*sys.argv[1:])