E13: real-weight model speciation — the Git Re-Basin residual confirms E12

The real-weight image of E12, and the answer to the mode-connectivity reviewer.
Small no-BN MLPs on MNIST, forked from a shared base and trained independently,
are weight-averaged; we measure the linear-mode-connectivity barrier before and
after in-house deterministic Git Re-Basin permutation alignment (neural/rebasin.py,
scipy linear_sum_assignment), decomposing it into removable (coordinate artefact)
and residual (reproductive isolation). kind: speciation_real.

Result (3 reps):
- shared (same task, shared fork): no barrier — trivially mergeable.
- independent (same task, different init): naive 0.056, alignment removes 98%
  (residual 0.001) — the incompatibility is a coordinate artefact.
- conflict (conflicting label maps): naive 0.496, alignment removes 0% (residual
  0.496) — genuine reproductive isolation. Because alignment demonstrably works on
  the independent case, the conflict residual is real, not a failure to align.
- Isolation cliff (speciation_real_cliff): residual rises 0.00->0.13->0.19->0.28->
  0.40->0.49 with the fraction of conflicting classes — the real-weight mirror of
  E12's cliff; residual==naive throughout (functional, not coordinate).

rebasin.py sanity-gated (recovers a known permutation exactly). plot_speciation_real.py
(2-panel), +4 pure-NumPy tests (142 green), README with honest positioning vs
Git Re-Basin / Entezari / Frankle / Pari 2024 / Zhou 2026. Wired into make mnist
(needs torchvision).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

figures/plot_speciation_real.py

@@ -0,0 +1,67 @@
+"""E13 figure — real-weight model speciation with Git Re-Basin.
+
+(A) The barrier decomposition per condition: the linear-mode-connectivity error barrier between two
+merged MLPs, split into the part permutation alignment REMOVES (coordinate artefact) and the RESIDUAL it
+cannot (reproductive isolation). `shared` ≈ 0; `independent` (same task, different init) is almost all
+removable (residual ≈ 0 — same species, different basis); `conflict` (conflicting tasks) is almost all
+residual (real isolation). (B) The isolation cliff: residual barrier vs the fraction of conflicting
+classes — the real-weight image of E12's cliff, after alignment (so it is not a coordinate artefact).
+
+Usage:  python figures/plot_speciation_real.py
+"""
+
+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  # noqa: E402
+
+
+def main() -> None:
+    dec, _ = load_bundle("results/speciation_real")
+    cliff, _ = load_bundle("results/speciation_real_cliff")
+
+    fig, axes = plt.subplots(1, 2, figsize=(13, 5))
+
+    # Panel A: removable (coordinate artefact) vs residual (isolation), stacked, per condition.
+    ax = axes[0]
+    order = [c for c in ["shared", "independent", "conflict"] if c in set(dec["condition"])]
+    g = dec.groupby("condition").agg(removable=("removable", "mean"),
+                                     residual=("residual", "mean")).reindex(order)
+    x = np.arange(len(order))
+    ax.bar(x, g["removable"], 0.6, label="removable by alignment\n(coordinate artefact)", color="#9ecae1")
+    ax.bar(x, g["residual"], 0.6, bottom=g["removable"], label="residual after alignment\n(reproductive isolation)",
+           color="#d62728")
+    ax.set_xticks(x); ax.set_xticklabels(order)
+    ax.set(ylabel="linear-mode-connectivity error barrier",
+           title="Merge barrier = coordinate artefact + residual isolation\n"
+           "(same task even across inits is coordinate; conflict is real)")
+    ax.legend(frameon=False, fontsize=8)
+
+    # Panel B: the isolation cliff — residual barrier vs conflict fraction.
+    ax = axes[1]
+    cg = cliff.groupby("conflict_frac").agg(res_m=("residual", "mean"), res_s=("residual", "std"),
+                                            nai_m=("barrier_naive", "mean")).reset_index()
+    ax.plot(cg["conflict_frac"], cg["nai_m"], "--o", color="#999", lw=1.4, label="naive barrier")
+    ax.plot(cg["conflict_frac"], cg["res_m"], "-o", color="#d62728", lw=2, label="residual (after alignment)")
+    ax.fill_between(cg["conflict_frac"], cg["res_m"] - cg["res_s"], cg["res_m"] + cg["res_s"],
+                    color="#d62728", alpha=0.15)
+    ax.set(xlabel="fraction of classes with conflicting labels", ylabel="error barrier",
+           ylim=(-0.02, None),
+           title="The reproductive-isolation cliff, in real weights\n"
+           "(residual rises with task conflict — not removable by alignment)")
+    ax.legend(frameon=False, fontsize=9)
+
+    fig.suptitle("E13 — real-weight model speciation: what permutation alignment can and cannot merge",
+                 y=1.02, fontsize=13)
+    fig.tight_layout()
+    savefig(fig, "results/speciation_real", "speciation_real")
+
+
+if __name__ == "__main__":
+    main()