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>

results/speciation_real_cliff/manifest.json

@@ -0,0 +1,18 @@
+{
+  "experiment": "speciation_real_cliff",
+  "master_seed": 13,
+  "git_commit": "56f642e7f9ae01fe01d863bdffe98b226b9dbb7b",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0",
+    "torch": "2.12.1",
+    "torchvision": "0.27.1"
+  },
+  "rows": 18,
+  "results_sha256": "0252581d848376ad698f56d4e69edbcae40cf5a0f090203d6f723cfc5e25303c",
+  "layer": "1.5",
+  "tier": "speciation_real"
+}

results/speciation_real_cliff/resolved_config.yaml

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+experiment: speciation_real_cliff
+seed: 13
+n_replicates: 3
+source_config:
+  experiment: speciation_real_cliff
+  kind: speciation_real
+  seed: 13
+  n_replicates: 3
+  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