Layer 1 core: Wright-Fisher knowledge-transmission model with E1-E2

Scaffold plus the Layer 1 analytical core and the first two experiments.

- knowledge/: truth, metrics, teachers (2.7.1 shared-switch construction),
  step, lineage, experiment, config, seeding (imported as `knowledge`).
- Validation spine green: neutral decay (Pred 1), fixation (Pred 2), exact
  mutation-drift equilibrium (Pred 3), union coverage (Pred 5). 68 tests pass.
- E1 reproduces tail-first collapse. E2 delivers the headline: a grounding
  phase boundary g* << 1, with stationary H tracking the exact H_eq closed
  form (g=0.005 -> 68% of truth diversity; g=0.05 -> 96%).
- Reproducibility: uv venv from a hash-pinned uv.lock is the source of truth;
  every run writes results.parquet + resolved_config.yaml + manifest.json
  (lib versions, git commit, sha256). Figures and manifests tracked; the
  large regenerable parquet is gitignored.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Makefile

@@ -0,0 +1,22 @@
+# Layer 1 automation. The uv venv (built from the committed uv.lock) is the
+# reproducibility source of truth; every target runs inside it via `uv run`.
+
+.PHONY: env test layer1 figures clean
+
+env:               ## build .venv from the committed lockfile
+	uv sync --extra dev
+
+test:              ## correctness tests + scientific-validation tests (the spine of trust)
+	uv run pytest
+
+layer1:            ## run experiments (E1-E2 done; E3-E6 appended as implemented)
+	uv run python -m knowledge.experiment configs/layer1/E1.yaml
+	uv run python -m knowledge.experiment configs/layer1/E2.yaml
+
+figures:           ## regenerate figures from committed results
+	MPLBACKEND=Agg uv run python figures/plot_E1.py
+	MPLBACKEND=Agg uv run python figures/plot_E2.py
+
+clean:             ## remove caches and generated results (keeps committed manifests)
+	rm -rf .pytest_cache **/__pycache__
+	find results -type f ! -name '.gitkeep' -delete 2>/dev/null || true