ArrayTrain (plan §12): simurg train — EGT cluster files from a cohort's GTCs

- simurg/train/clusters.py: vectorised per-locus θ mixture (AA/AB/BB + outlier component, θ-ordered bounds),
  cluster selection and merging, lone clusters homozygous, missing clusters imputed by cross-locus regression
  per assay type, cluster_sep and train (GenTrain-field) scores.
- formats/egt.py: write_egt (EGT v3, data block 9, round-trips through the reader).
- pipeline/train.py: normalised θ/R from GTC raw X/Y + transforms, sex-aware (X females, Y males, MT haploid),
  intensity-only loci as one R cluster.
- scripts/train/concordance_chr.py: array vs 1000G 30x on one chromosome.
Demo (36 GSA v4 PGx arrays, chr22 vs 1000G): trained 99.29 % / NRD 2.6 % vs vendor EGT 99.57 % / 1.55 %.

docs/messages.md

@@ -75,6 +75,7 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_SHEET_NO_KEY_COLUMNS` | error | Sample sheet lacks SentrixBarcode_A/SentrixPosition_A | IN-002 |
 | `E_SHEET_RESERVED` | error | Sample sheet column collides with an output column | IN-005 |
 | `E_SHEET_TOO_LONG` | error | Sample sheet name or value longer than 500 characters | IN-006 |
+| `E_TRAIN_TOO_SMALL` | error | Too few GTCs to train a cluster file | plan §12 |
 | `I_CN_SEX_RESOLVED` | info | Sample sex updated from U by the caller | CYTO-024 |
 | `I_UNLISTED_IDATS` | info | IDAT pairs not listed in the sample sheet are ignored | IN-016 |
 | `W_CN_NO_FASTA` | warning | No FASTA: VCF REF padding bases written as N | CYTO-029 |