- **`SpilloverDiD(survey_design=SurveyDesign.subpopulation(...))` full-design retention via zero-pad scores (Wave E.3).** Closes the Wave E.1/E.2/follow-up documented limitation at `REGISTRY.md:3249`: `SurveyDesign.subpopulation()`-derived designs AND warn-and-drop fits now preserve the full-domain resolved survey design — `n_psu` / `n_strata` / `df_survey` / Binder TSL per-stratum centering reflect the FULL domain rather than the post-`finite_mask` fit sample. **Documented synthesis (library-convention adoption, NOT new methodology):** Wave E.3 adopts the canonical "zero-pad scores to full panel + retain full-design resolved survey" pattern from R `survey::svyrecvar(subset())` (Lumley 2010 §2.5) already established in `diff_diff/imputation.py:2175-2183` (PreTrendsImputation lead regression — Omega_0 scores zero-padded back to full panel length) and `diff_diff/prep.py:1401-1432` (DCDH cell variance — IF zero-padded outside the cell). Wave E.3 propagates the same convention to SpilloverDiD's Wave E.1 Binder TSL × Wave D Gardner GMM × Wave E.2/follow-up stratified-Conley + serial Bartlett meat. **Mechanical realization (one new `_compute_gmm_corrected_meat` kwarg):** the gamma_hat / Psi build stays on SURVEY-FINITE-MASK inputs (`X_1_sparse_fit`, `X_10_sparse_fit`, `eps_10_fit` built on `survey_finite_mask = finite_mask & survey_weights > 0`; `X_2_kept_gamma`, `eps_2_fit_gamma`, `survey_weights_fit_gamma` projected from the fit-sample frame down to survey_finite_mask) so the drop-first stage-1 FE column space is bit-identical to the pre-E.3 path. `_compute_gmm_corrected_meat` gains a new optional kwarg `score_pad_mask: Optional[np.ndarray] = None`: when supplied, the helper zero-pads the fit-sample `Psi` to full panel length AFTER construction but BEFORE kernel dispatch via `Psi_padded[score_pad_mask] = Psi`. Kernel-dispatch arrays (`cluster_ids`, `conley_coords`, `conley_time`, `conley_unit`, `resolved_survey`) are passed at FULL length so the meat helpers (Binder TSL / stratified-Conley / serial Bartlett) see the full-domain PSU / strata / centroid / time geometry. The `_validate_conley_kwargs` call inside the helper reads `n_for_conley = len(score_pad_mask)` when the kwarg is set so the Conley shape checks see the full-length geometry. **`gamma_hat` invariance:** the gamma_hat solve operates on fit-sample inputs throughout — bit-identical to the pre-E.3 path (critical for the case where `_build_butts_fe_design_csr`'s `pd.factorize` re-compaction would drop a different unit's column under a full-length FE build than under a fit-length one). **Bread invariance:** `A_22 = X_2_kept' W X_2_kept` at `spillover.py:3187-3214` still uses fit-length `X_2_kept` because `A_22_full = X_2_full' W_full X_2_full` equals `A_22_kept` when zero-weight rows contribute zero. **A2 invariant:** warn-and-drop and `SurveyDesign.subpopulation()` drops are treated identically — both apply the zero-pad mechanism. The "both mechanisms compose cleanly" case (subpop-excluded row that is ALSO warn-and-dropped) produces `Psi = 0` from either cause; the PSU still counts toward `n_psu_full`. Hand-computation methodology anchor at `_scratch/wave_e3_smoke.py` codifies the A2 invariant on 4 PSU × 4 period × 3 obs synthetic. **Subpopulation parity vs upstream-subset:** `df_survey` matches the full domain regardless of how many rows the subpopulation mask excludes (mirrors R `svyglm(design=subset(d, mask))` vs `svyglm(design=svydesign(data=data[mask], ...))`). SE may differ by design — subpopulation retains zero-padded PSU geometry; upstream-subset drops PSUs entirely. **Pre-E.3 baseline parity:** when `finite_mask.all() == True` AND all weights `> 0`, the Wave E.3 zero-pad is a no-op — ATT + SE + n_psu + df_survey match pre-E.3 baseline values via FIXED GOLDEN values at `test_c` (`rtol=1e-12, atol=1e-12`). **Cross-surface n_psu consistency:** top-level `res.n_psu` reads from `len(resolved_survey_fit.weights)` on the implicit-PSU branch (was `int(finite_mask.sum())` pre-codex-R1-P2-fix); this keeps `res.n_psu == res.survey_metadata.n_psu` on weights-only / strata-only survey designs under warn-and-drop. Regression at `test_c2`. **Restrictions inherited:** replicate-weight variance + subpopulation continues to raise `NotImplementedError` at the Wave E.1 gate. TwoStageDiD's analogous `finite_mask + design-subset` pattern at `two_stage.py:567-601` is NOT yet adopted to Wave E.3 — separate parity follow-up tracked in `TODO.md` (an expected-divergence test was attempted but TwoStageDiD's always-treated handling at `two_stage.py:294-336` differs from SpilloverDiD's per-unit Omega_0 check, so the divergence didn't materialize on the standard fixture; the parity follow-up should add its own targeted regression). **Implementation:** `spillover.py:2845-2896` design-subset block deleted; `survey_weights_fit = survey_weights[finite_mask]` retained for the stage-2 OLS solve which still operates on the fit sample; `cluster_ids_full[finite_mask]` subset dropped on the survey path. `_compute_gmm_corrected_meat` call at `spillover.py:3163` now receives FIT-LENGTH gamma_hat-construction inputs (unchanged) plus FULL-LENGTH kernel-dispatch arrays (`cluster_ids_for_meat`, `conley_*_for_meat`, `resolved_survey_fit`) plus the new `score_pad_mask=survey_finite_mask` kwarg; no-survey path passes `score_pad_mask=None` and uses fit-length variables throughout (bit-identical to pre-E.3). `_compute_gmm_corrected_meat` at `two_stage.py:62-80` adds one new optional kwarg `score_pad_mask: Optional[np.ndarray] = None` and one post-Psi-construction zero-pad block; the `_validate_conley_kwargs` call uses `n_for_conley = len(score_pad_mask)` when the kwarg is set. Within-unit-constancy validator at `spillover.py:2913` updated to operate on full-length unit array. Second `compute_survey_metadata` recompute at `spillover.py:2954-2959` uses full-length `raw_w`. No `_compute_stratified_meat_from_psu_scores` / `_compute_stratified_conley_meat` / `_compute_stratified_serial_bartlett_meat` signature changes. **Tests:** new `TestSpilloverDiDWaveE3SubpopulationFullDesign` and `TestSpilloverDiDWaveE3SubpopulationFullDesignEventStudy` classes in `tests/test_spillover.py` (19 tests: pre-E.3 baseline parity via pinned goldens, n_psu cross-surface consistency on implicit-PSU branch, A2 invariant (zero-pad mechanics via mock-spy), subpopulation × explicit-PSU parity, conley + lag>0 + subpopulation × explicit-PSU / cluster-injection / weights-only branches, cluster-as-PSU + subpopulation parity, unit with BOTH zero weight AND no Omega_0 support, gamma_hat-build sample excludes zero-weight rows, n_obs / n_treated / n_control / n_far_away_obs reflect count_mask, warn-drop SE drift golden, ATT bit-equality under PSU-last-sort exclusion, exact event-study n_obs propagation, event-study on both is_staggered branches with analytical + conley+lag variants). Pre-existing Wave E.1 `test_p2_finite_mask_forces_drop_under_survey` assertion flipped from `n_psu=8` (subset) to `n_psu=10` (full domain) to reflect the new contract.
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