qc: add mt_deletion_scan first-pass mtDNA deletion scan

Junction scan over realigned mitochondrial BAMs: same-strand split alignments with a
reference gap and long CIGAR deletions, clustered per sample on both breakpoints and
reported with two or more supporting reads, with a rough deletion fraction from the
depth at the breakpoints. Run on the rescued human blood and Letizia mouse sets on
2026-09-06: no supported junction in either cohort; documented under
docs/pipeline_notes.md#numt_rescue (verification tools).

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