pipeline: add RESCUE_MT process

Opt-in step-2 process (params.rescue_mt, params.numt_bed) that rebuilds the MT-only
BAM from the unfiltered whole-genome BAM: primary records on the mitochondrial contig
or on any NUMT locus are realigned to the contig alone with their modification tags,
reads with 300 or more unaligned bases are dropped, and step 3 uses the result in
place of EXTRACT_MT. RESCUE_MT_SUMMARY aggregates the per-sample diagnostics and
stops the run when clip-dropped NUMT-origin reads exceed rescue_max_numt_frac.

Ships the tools the process and the acceptance checks run on (src/bin/rescue_mt.sh,
derive_numt_loci.sh, mt_depth_compare.sh, mt_site_compare.sh,
mt_supplementary_check.sh, mt_read_accounting.sh, mt_pileup_check.sh) and the NUMT
reference data for GRCm39 and GRCh38 (references/numt/<build>/), with their
derivation recorded in docs/pipeline_notes.md#numt_rescue. Enabled for
letizia_mouse; off for human_blood.

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