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).

src/simurg/pipeline/cn.py

@@ -392,7 +392,7 @@ def call_sample(si: SampleInput, ctx: dict[str, Any], opts: CnCallOptions) -> di
             post = hmm.forward_backward(e, sw, prior)
             evs = extract(chrom, path, states, p)
             for ev in evs:
-                annotate_stats(ev, p, x_raw, b, gt, post, states, m_sp, ctx["gamma"], haploid)
+                annotate_stats(ev, p, x_raw, b, gt, post, states, m_sp, ctx["gamma"], haploid, baf_sd, pfb[idx])
             evs = post_filter(evs, [x_raw[ev.i0 : ev.i1] for ev in evs], th, counts)
             for s_, e_ in _runs(path):
                 st = states[int(path[s_])]