docs: update examples to use hg38 as primary reference genome (#1046)

• docs: update examples to use hg38 as primary reference genome

hg38/GRCh38 data files were added in PR #837 but documentation still defaulted to hg19 examples. Update pipeline, quickstart, nonhybrid, and scripts docs to show hg38 as the primary reference while noting hg19 files remain available for legacy workflows.

Ref #822

• fix: correct UCSC mappability link for hg38

hg38 does not have an encodeDCC/wgEncodeMapability directory on UCSC. Point to the hg38 bigZips directory for current data, and keep the hg19 ENCODE link for legacy workflows.