P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen

- gtc-to-vcf --info-fields ASSAY_TYPE,NORM_BIN,GENTRAIN,CLUSTER_SEP,ILMN_STRAND,PROBE_IDS (--egt) and
  --extra-format X,Y,NORMX,NORMY,THETA,R, in per-sample VCFs and the --merge BCF (OUT-012, plan §8.3);
  equal to gtc2vcf's values (THETA/R missing where both normalized intensities are 0, K-023)
- --merge-snv-indel (OUT-021, EDGE-013): alleles extended to the longest REF; SNV probes read the base at POS
- --auxiliary-loci (OUT-035, EDGE-015): rules (a)-(e), E_AUX_INVALID; rule (d) uses the last plus-strand base
  for minus-strand designs (spec amended, as GTCtoVCF)
- export plink --format bed|pgen|both: PLINK 2 fixed-width .pgen/.pvar/.psam; plink2 reads it back to a .bed
  byte-identical to ours
- cohort store keeps raw/normalized intensities for the BCF path; tests (unit + gtc2vcf oracle); docs

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

README.md

@@ -17,7 +17,8 @@ KING-robust relatedness, Mendelian errors, locus summary and a self-contained HT
 1000 Genomes samples all 717 pedigree parent–offspring pairs are recovered and trio Mendelian error rates are ~0.03 %
 (`docs/validation/P5.md`).
 Phase **P6 (outputs)** is complete: `simurg gtc-to-vcf` (plus-strand harmonisation with audit, merged multi-probe
-sites, per-sample VCF.gz + tabix or a cohort BCF + CSI) and `simurg export plink|bedgraph|finalreport|locus-summary`.
+sites, per-sample VCF.gz + tabix or a cohort BCF + CSI, optional INFO/intensity fields, SNV+indel merging, MNV
+auxiliary loci) and `simurg export plink|bedgraph|finalreport|locus-summary` (PLINK 1 `.bed` and PLINK 2 `.pgen`).
 On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained differences and PLINK files match plink2
 (`docs/validation/P6.md`).
 Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`,