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

src/simurg/core/errors.py

@@ -85,6 +85,7 @@ CATALOGUE: dict[str, MessageDef] = dict(
         _m("E_BPM_FORMAT", "error", "BPM manifest is malformed or unsupported", "IN-040"),
         _m("E_CSV_MANIFEST_FORMAT", "error", "CSV manifest is malformed", "IN-041"),
         _m("E_BPM_CSV_MISMATCH", "error", "BPM and CSV manifests describe different loci", "IN-042"),
+        _m("E_EGT_MANIFEST_MISMATCH", "error", "Cluster file lacks loci of the manifest", "IN-043"),
         _m("E_EGT_LOAD", "error", "Cluster (EGT) file cannot be loaded", "IN-044"),
         _m("W_EGT_NAME", "warning", "Cluster file name is not portable", "IN-045"),
         _m("W_MANIFEST_NO_REFSTRAND", "warning", "Manifest lacks RefStrand annotation", "IN-040"),