fix(modkit): drop --seed (it forced --sampling-frac on small mtDNA BAMs)

The full run failed at MODKIT: 'modkit extract calls' aborted with 'required: --sampling-frac' because --seed makes modkit assume fractional sampling. Confirmed via --help on the container. Removed --seed from extract/pileup/summary and removed the now-orphan modkit_seed param. Every barcode has <10042 reads (Nanopore long-read, ~100-500/barcode), so modkit's default sampling uses ALL reads and the 10th-percentile threshold is deterministic without a seed (the 'Only sampled 197 reads' line is an informational warning, not an error). EXTRACT_MT/DOWNSAMPLE_MATCH/MUTSERVE already ran, so -resume reuses them on the re-run.