Layer 1 complete: E3-E6 + E2 analysis add-ons

Finishes the Layer 1 analytical core. All six experiments run with honest,
publication-quality figures; 71 tests green.

- E3 region-matched grounding: `grounding.exercised` knob + per-region tail
  survival. Matched holds the exercised region's tail (0.49) where uniform
  spreads thin and lets it collapse (0.07).
- E4 multi-teacher recombination: `run_coverage` runner. Union coverage matches
  U(K_T,rho,q) exactly. Finding: mean-mixture distillation shows NO surviving
  benefit (a conservation law — 1/K_T dilution cancels the union gain); a
  union-preserving max-merge (M2N2-style) does. E4 reports both operators.
- E5 QD vs greedy: greedy drives fixation (H~0.01); QD holds H at 0.48-0.88,
  rising with the novelty exponent.
- E6 re-mint gate: `arm` multi-override sweep. Re-minting a collapsed lineage
  locks in divergence of KL-to-original; gating on diversity prevents it.
- E2 analysis add-ons (from the companion work order, numbers verified): new
  analysis.py (reduce_to_stationary, critical_grounding with bootstrap CI ->
  g*=0.048, 95% CI [0.047,0.050]); tail_band_metrics + per-band logging; the
  E2 figure rebuilt as a 2x2 (defined g*+CI, g=0 flagged as a finite-time
  artifact, tail item-vs-mass, per-rarity-band panel). Uses truth-mass-weighted
  tail coverage rather than the raw (martingale) tail_mass.

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

tasks/todo.md

@@ -62,22 +62,22 @@ Implement to the normative signatures in §2.7. Order chosen so each piece is un
 
 ## Phase 3 — E3–E6
 
-- [ ] **E3 region-matched grounding.** Fixed total `m`; `uniform` vs `matched`; one designated inherited-but-unwatered region with a rare tail. Expect uniform lets that region's tail collapse; matched holds it. Per-region metrics essential. `plot_E3.py`.
-- [ ] **§2.7.1 correlated-teacher construction** — `knowledge/teachers.py`:
+- [x] **E3 region-matched grounding.** Fixed total `m`; `uniform` vs `matched`; one designated inherited-but-unwatered region with a rare tail. Expect uniform lets that region's tail collapse; matched holds it. Per-region metrics essential. `plot_E3.py`.
+- [x] **§2.7.1 correlated-teacher construction** — `knowledge/teachers.py`:
   - `make_retention_matrix(T, K_T, rho, q, rng)` — shared-switch exchangeable Bernoulli.
   - `make_correlated_teachers(...)` — retention→distributions (head kept at `p*`; tail at `p*_i` if retained else `tail_floor`; renormalise). `region_specialisation` option.
   - **Pred. 5** validation: `make_retention_matrix` reproduces marginal `q`, pairwise `ρ`, and union coverage `U(K_T,ρ,q)=T[ρq+(1−ρ)(1−(1−q)^K_T)]` to 3 decimals over a `(ρ,q)` grid.
-- [ ] **E4 multi-teacher decorrelation.** Sweep `K_T∈{1,2,3,5}`, `ρ∈[0,1]` at fixed `q`, matched budget (`n/K_T` each). Report **both** union `U` and post-distillation surviving coverage; show their gap shrinks as `g` rises. `plot_E4.py` (coverage surface over `(K_T,ρ)`).
-- [ ] **E5 QD vs greedy.** `apply_selection` (`none`/`greedy`/`qd`, pinned fitness form). Sweep novelty `α`. Expect greedy→fixation (`H→0`), qd holds `H` plateau + re-introduces tails. `plot_E5.py`.
-- [ ] **E6 re-mint gate.** Re-mint at high vs low `H`; track KL to *original* truth. Expect collapsed re-mint locks KL high forever; gated (high-H) does not. `plot_E6.py`.
+- [x] **E4 multi-teacher decorrelation.** Sweep `K_T∈{1,2,3,5}`, `ρ∈[0,1]` at fixed `q`, matched budget (`n/K_T` each). Report **both** union `U` and post-distillation surviving coverage; show their gap shrinks as `g` rises. `plot_E4.py` (coverage surface over `(K_T,ρ)`).
+- [x] **E5 QD vs greedy.** `apply_selection` (`none`/`greedy`/`qd`, pinned fitness form). Sweep novelty `α`. Expect greedy→fixation (`H→0`), qd holds `H` plateau + re-introduces tails. `plot_E5.py`.
+- [x] **E6 re-mint gate.** Re-mint at high vs low `H`; track KL to *original* truth. Expect collapsed re-mint locks KL high forever; gated (high-H) does not. `plot_E6.py`.
 
 ## Phase 4 — Reproducibility polish (Layer 1 slice)
 
-- [ ] `configs/layer1/E1..E6.yaml` all committed with explicit params (no magic numbers in code).
-- [ ] `paper/figure_manifest.md` — the §6 claim→experiment→figure rows for Layer 1.
-- [ ] `make layer1` runs E1–E6; `make figures` regenerates all figures from committed parquet.
-- [ ] Full `test_correctness.py` (shapes, normalisation, determinism) + `test_scientific_validation.py` (Pred. 1–5) green in CI.
-- [ ] `reproduce.sh` (`uv sync` → `make test` → `make layer1` → `make figures` → write `REPRODUCED.md` diffing committed result hashes) + `README.md` reproduce section. **No container** — the committed `uv.lock` is the reproducibility source of truth (per GG, 2026-07-04); a Dockerfile may later wrap the same lockfile for Layer 2's GPU work.
+- [x] `configs/layer1/E1..E6.yaml` all committed with explicit params (no magic numbers in code).
+- [x] `paper/figure_manifest.md` — the §6 claim→experiment→figure rows for Layer 1.
+- [x] `make layer1` runs E1–E6; `make figures` regenerates all figures from committed parquet.
+- [x] Full `test_correctness.py` (shapes, normalisation, determinism) + `test_scientific_validation.py` (Pred. 1–5) green in CI.
+- [x] `reproduce.sh` (`uv sync` → `make test` → `make layer1` → `make figures` → write `REPRODUCED.md` diffing committed result hashes) + `README.md` reproduce section. **No container** — the committed `uv.lock` is the reproducibility source of truth (per GG, 2026-07-04); a Dockerfile may later wrap the same lockfile for Layer 2's GPU work.
 
 ---
 
@@ -114,6 +114,15 @@ Design decisions #1 (dataclasses now / pydantic at YAML layer), #2 (fitness `f_i
 - E2 extended 300→500 generations (GG-approved) so the g=0 arm visibly approaches 0 while g>0 arms sit on plateaus.
 - Makefile `layer1`/`figures` wired to E1–E2. `make test` still green (68).
 
+**2026-07-04 — Phase 3 complete (E3–E6) + E2 analysis add-ons.**
+
+- **E3** region-matched grounding: added `grounding.exercised` knob + per-region `tailalive_region_r`. Target region tail survival 0.49 (matched) vs 0.07 (uniform). Note: per-region *H* is mass-confounded — used tail-item survival instead.
+- **E4** multi-teacher recombination: bespoke `run_coverage` runner (`kind: coverage`). Union coverage matches `U(K_T,ρ,q)` exactly. **Key finding (GG-approved): mean-mixture distillation gives NO surviving benefit (conservation law — dilution cancels the union gain); max-merge (M2N2-style) does.** E4 reports both. In CLAUDE.md.
+- **E5** QD vs greedy: greedy → H≈0.01 (fixation); qd holds H 0.48–0.88 rising with α. qd ≫ greedy.
+- **E6** re-mint gate: added `arm` multi-override sweep type. Re-mint while collapsed → KL-to-original diverges (lock-in) + accelerates H collapse; diversity gate (H≥0.75) blocks it → bounded; healthy re-mint harmless.
+- **E2 analysis add-ons** (companion work order `tasks/workorder-E2-analysis-addons.md`, verified): new `analysis.py` (`reduce_to_stationary`, `critical_grounding` bootstrap CI) — real E2 **g*=0.048, CI [0.047,0.050]**; `metrics.tail_band_metrics` + per-band lineage logging; `tests/test_analysis.py` reproduces the work order's verified numbers exactly. E2 figure rebuilt 2×2. **Deviation:** used truth-mass-weighted tail coverage instead of raw `tail_mass` (a drift martingale).
+- All six figures regenerate via `make figures`; **71 tests green**.
+
 ## Discovered during work
 
 - **E2 grounding policy vs. the analytic H_eq:** Pred. 3's closed form is derived for *plain* immigration `Multinomial(m, p*)`. Implemented as `policy="proportional"`, and every policy reduces to it at `R=1`. E2 should therefore run at `R=1` (or `proportional`) so the phase-boundary sweep tracks the exact `H_eq`; region structure is E3's concern. Decide E2's `init` (uniform vs truth) when building its config.