P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype

- genotype/clusters.py: EGT aligned to manifest order (float32 mean R)
- genotype/gencall.py: flair, six-case likelihood, priors/posteriors,
  fuzzy sub-scores and score map, vectorised with the reference's
  float/double evaluation order and libm transcendentals
- genotype/baf_lrr.py, sex.py (rules v1/v2), sample.py (IDAT -> Gtc)
- pipeline/inputs.py shared by ingest and genotype
- pipeline/genotype.py + CLI: GTC per sample, sample_summary.tsv/json
  (OUT-060..063), run manifest
- GTCs from IDATs are byte-identical to the oracle for 36 GSA samples x
  2 normalization versions (NaN sign canonicalised to the x86 pattern)

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

docs/messages.md

@@ -12,6 +12,7 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_DUP_GTC` | error | Several GTC files resolve to the same sample | IN-030 |
 | `E_DUP_IDAT` | error | Several IDAT pairs resolve to the same sample | IN-022 |
 | `E_EGT_LOAD` | error | Cluster (EGT) file cannot be loaded | IN-044 |
+| `E_EGT_MANIFEST_MISMATCH` | error | Cluster file lacks loci of the manifest | IN-043 |
 | `E_FILE_NOT_FOUND` | error | Input file or folder does not exist | CLI-016 |
 | `E_FILE_UNREADABLE` | error | Input file cannot be read | CLI-016 |
 | `E_GTC_CORRUPT` | warning | GTC file failed validation; sample skipped | IN-032 |