CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness

Mosaic fraction from the BAF split now subtracts the heterozygous BAF noise (median |BAF-0.5| of unsplit
hets = 0.6745 sigma_b), and a mosaic loss lacking its expected heterozygotes gets MF 1 and is promoted to a
constitutional DEL (CYTO-020). Adds scripts/v2/cn_tune.sh + cn_tune_report.py (GSE165845 rounds on the Pi).

SIMURGARRAY_FUNCTIONAL_SPEC.md

@@ -2435,6 +2435,16 @@ about **algorithms or numerics**, the plan wins. Each such conflict found during
 
   Each yields valid, possibly empty, VCF and JSON output (EDGE-024). (src: E-35)
 
+- **CYTO-041** `§10.3 · v2` **MF refinements [OURS].** Two refinements of CYTO-018, from real-data validation
+  (docs/validation/V2_cn.md, K-027):
+  - *noise-corrected split:* the median |BAF − 0.5| of unsplit heterozygotes is 0.6745·σ_b (σ_b = the sample's
+    heterozygous BAF SD), so `d = √max(0, d_obs² − (0.6745·σ_b)²)`. Without this, noise alone gave MF ≈ 0.2 in
+    diploid regions and waves were called as mosaic losses.
+  - *complete loss:* a mosaic loss with ≥ 20 finite-BAF probes, ≥ 5 expected heterozygotes (Σ 2p(1−p) over PFB p),
+    and fewer than 0.25 × expected probes with 0.1 < BAF < 0.9 has MF = 1. With the default
+    `--max-mosaic-fraction 1.0` it is therefore promoted (CYTO-020) to a constitutional DEL with `HIGHFRACTION`.
+    This catches constitutional deletions whose LRR is compressed towards the mosaic states.
+
 ---
 
 ## 7. Targeted PGx copy number (v2)
@@ -3710,6 +3720,7 @@ Generated from the item tags (`build.py`). Phases: P0–P10 as in plan §18; `v2
 | CYTO-038 | Model building | §10 | v2 | A-G52 |
 | CYTO-039 | Batch scale | §10, §19 | v2 | D-9, E-35 |
 | CYTO-040 | Degenerate samples | §10 | v2 | E-35 |
+| CYTO-041 | MF refinements | §10.3 | v2 | K-027 |
 | PCN-001 | Region catalogue | §11 | v2 | B-23, C-G25, D-10 |
 | PCN-002 | Genotype every region [EMU] | §11 | v2 | B-23 |
 | PCN-003 | Inputs | §11 | v2 | A-G37 |