qc: add mt_coverage_profile tool

Per-window depth profile of the mitochondrial contig from the modkit pileups, with a
per-sample gap table and a figure. Exit status 2 when some window is below the
minimum in every sample, the signature of a near-identical NUMT dropping authentic
reads at the MAPQ filter. Sample ids follow the pipeline convention (token before
the first dash) and --run-id filters the samplesheet to one run. Documented in
docs/pipeline_notes.md#mt_coverage_profile.

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