docs: record the NUMT failure mode and the rescue design

Whole-genome alignment fails as a NUMT defence when a nuclear copy is near-identical
to mtDNA: reads contained in the copied segment tie, get MAPQ 0, and the step-2
filter removes them. Records the mouse chr1 copy (chrM 6,393-11,042, 99.96 percent
on GRCm39), the derivation of NUMT loci per build, the rescue by realignment of
chrM and NUMT-locus reads to the mitochondrial contig alone, the filter on unaligned
bases that separates nuclear flanks from adapters, the decision rule, the handling
of split reads at the origin, and the measured outcome on the three projects.

Co-Authored-By: Claude Fable 5.1 <[email protected]>