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_E5.py

@@ -1,79 +0,0 @@
-"""E5 figure: quality-diversity vs greedy selection.
-
-At matched grounding, greedy (directional) selection drives the lineage toward the
-fittest items and collapses diversity, while quality-diversity selection (a novelty bonus
-w_i ∝ f_i·p_i^{-alpha}) maintains a high stationary heterozygosity that rises with the
-novelty exponent alpha. Usage:  python figures/plot_E5.py [results/E5]
-"""
-
-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
-
-
-def main(results_dir: str = "results/E5") -> None:
-    df, cfg = load_bundle(results_dir)
-    last = int(cfg["generations"] * 0.8)
-
-    def arm(mode, alpha=1.0):
-        return df[(df["mode"] == mode) & (df["novelty_alpha"] == alpha)]
-
-    fig, axes = plt.subplots(1, 3, figsize=(15, 4.3))
-
-    # Panel 1: H trajectories
-    ax = axes[0]
-    series = [("greedy", 1.0, "#d62728", "greedy"),
-              ("qd", 1.0, "#ff7f0e", "quality-diversity (α=1)"),
-              ("qd", 2.0, "#1f77b4", "quality-diversity (α=2)"),
-              ("none", 1.0, "#2ca02c", "none (grounding only)")]
-    for mode, a, c, lab in series:
-        s = arm(mode, a).groupby("generation")["heterozygosity"].mean()
-        ax.plot(s.index, s.values, color=c, label=lab)
-    ax.set(xlabel="generation", ylabel="heterozygosity $H$",
-           title="Greedy collapses;\nquality-diversity maintains diversity")
-    ax.legend(frameon=False, fontsize=8)
-
-    # Panel 2: stationary H vs alpha for qd, with greedy/none reference lines
-    ax = axes[1]
-    qd = df[(df["mode"] == "qd") & (df["generation"] >= last)]
-    st = qd.groupby("novelty_alpha")["heterozygosity"].agg(["mean", "sem"])
-    ax.errorbar(st.index, st["mean"], yerr=1.96 * st["sem"], fmt="-o",
-                color="#ff7f0e", capsize=3, label="quality-diversity")
-    for mode, c in (("greedy", "#d62728"), ("none", "#2ca02c")):
-        h = arm(mode, 1.0)
-        h = h[h["generation"] >= last]["heterozygosity"].mean()
-        ax.axhline(h, ls="--", color=c, label=f"{mode}")
-    ax.set(xlabel=r"novelty exponent $\alpha$", ylabel="stationary $H$",
-           title="Quality-diversity keeps $H$\nabove greedy for all α")
-    ax.legend(frameon=False, fontsize=9)
-
-    # Panel 3: stationary support size per arm
-    ax = axes[2]
-    arms = [("greedy", 1.0, "greedy"), ("qd", 0.5, "quality-diversity α=0.5"),
-            ("qd", 1.0, "quality-diversity α=1"), ("qd", 2.0, "quality-diversity α=2"), ("none", 1.0, "none")]
-    labels, vals, errs, colors = [], [], [], []
-    palette = {"greedy": "#d62728", "qd": "#ff7f0e", "none": "#2ca02c"}
-    for mode, a, lab in arms:
-        s = arm(mode, a)
-        s = s[s["generation"] >= last]["support_size"]
-        labels.append(lab); vals.append(s.mean()); errs.append(1.96 * s.sem())
-        colors.append(palette[mode])
-    ax.bar(range(len(labels)), vals, yerr=errs, color=colors, capsize=3)
-    ax.set(ylabel="stationary support size", title="Surviving items per arm",
-           xticks=range(len(labels)))
-    ax.set_xticklabels(labels, rotation=25, ha="right", fontsize=8)
-
-    fig.tight_layout()
-    letter_axes(fig)
-    savefig(fig, results_dir, "E5")
-
-
-if __name__ == "__main__":
-    main(*sys.argv[1:])