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>

configs/neural/speciation_real_cliff.yaml

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+experiment: speciation_real_cliff
+kind: speciation_real
+seed: 13
+n_replicates: 3
+
+# E13 (cliff) — the real-weight reproductive-isolation curve, mirroring E12's isolation cliff. Two MLPs
+# forked from a shared MNIST base; child B learns a CONFLICTING label map on a fraction `conflict_frac`
+# of the classes (the rest agree). Sweeping the conflict fraction traces the residual (after-alignment)
+# barrier from 0 (no conflict = same species) to its maximum (full conflict = fully isolated) — the
+# real-weight image of "the isolation cliff rises with epistasis". Alignment is applied throughout, so
+# the curve is the residual that permutation cannot explain away.
+
+speciation_real:
+  sizes: [784, 512, 512, 10]
+  conflict_fracs: [0.0, 0.2, 0.4, 0.6, 0.8, 1.0]
+  t_div_fixed: 800
+  base_steps: 500
+  lr: 0.05
+  batch: 128
+  n_eval: 2000
+  data_root: data
+
+output:
+  dir: results/speciation_real_cliff