knowledge: learning kernel — model the estimator bias, not just sampling

Revisiting Layer 1 against Layer 1.5 (and Riis 2026, arXiv:2604.08554):
neutral Wright-Fisher is a null that BOTH neural architectures deviate
from, in opposite directions. Add a learning kernel to the refit step,
p_{t+1} = T_theta(counts/n), with two population-genetics knobs -- reset u
(mutation toward a prior = smoothing) and temperature tau (sharpening =
mode-competition) -- both identity by default, so the histogram bridge and
all 68 scientific-validation/correctness tests are unchanged.

Result: neutral drift fails both neural models, oppositely.
- VAE regime (n=6000, K=30): neutral drift is inert (no collapse), yet the
  real VAE collapsed to one mode. Sharpening tau=0.8 reproduces it -- the
  estimator ADDS collapse pressure.
- RNN regime (n=200, K=256): neutral drives H->0, but the real RNN only
  partially collapses. Mutation u=0.006 reproduces the H-floor -- the
  estimator REMOVES collapse pressure. Honest caveat: uniform-mutation
  overshoots the RNN's forward-KL, evidence its smoothing prior is
  truth-like, not uniform (future refinement).

This mechanistically explains the architecture-generality result and the
softened neural g*, and develops the estimator axis Riis names as future
work. New: knowledge/kernel.py, configs/layer1/kernel_{sharpen,smooth}.yaml,
figures/plot_kernel.py (overlays analytic arms vs committed neural
endpoints), READMEs, tests/test_kernel.py (+6, 105 total green). Strategic
Riis positioning recorded in CLAUDE.md: concede "collapse=drift" as prior
art; lead with recombination, the kernel axis, and the Lamarckian society.

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

Makefile

@@ -15,8 +15,8 @@ env-mnist:         ## add torchvision for the real-MNIST confirmation tier
 test:              ## correctness tests + scientific-validation tests (the spine of trust)
 	uv run pytest
 
-layer1:            ## run experiments E1-E6
-	for e in E1 E2 E3 E4 E5 E6; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done
+layer1:            ## run experiments E1-E6 + the learning-kernel bridge (analytic)
+	for e in E1 E2 E3 E4 E5 E6 kernel_sharpen kernel_smooth; do uv run python -m knowledge.experiment configs/layer1/$$e.yaml; done
 
 neural:            ## run Layer 1.5 synthetic neural experiments (excludes the heavy MNIST tier)
 	for c in configs/neural/*.yaml; do case "$$c" in *mnist*) ;; \