Update CRAM, SAM, and VCF PDFs

Regenerate PDFs with recent updates:
CRAM: container language tightening
SAMtags: recommend the MM:Z ? flag
SAMv1: new `@RG PL` platform field values
VCFv4.x: typo fix, MD5 calculation, (un)structured headers clarification
         (v4.3 also: BOM, 4.1 to 4.2 changes)

This commit does not update VCFv4.4.draft.pdf, in case the VCF maintainers
prefer to update that when a new release candidate is designated.

Author: jmarshall