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feat: add mtDNA heteroplasmy calling (mutserve2) in the step-3 sub workflow

João Henrique Chrusciel requested to merge feat/chrm-rescue into main

New src/modules/heteroplasmy.nf: EXTRACT_MT -> DOWNSAMPLE_MATCH -> MUTSERVE (native + coverage-matched arms) -> PARSE/MERGE, plus optional Haplocheck sample-contamination QC. Gated by --enable_heteroplasmy (default off); runs from the mtDNA-Server 2 container (mutserve 2.0.3). Reuses the existing whole-genome alignment: only chrM is extracted, no re-alignment. Coverage-matched at T=40x (cohort-derived) with a fixed downsample seed; 1/3/5/10% floors applied in R. Adds params (nextflow.config), wiring (MODKIT_AND_MULTIQC.nf), docs (pipeline_notes.md#heteroplasmy) and README entries.

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