VCF annotator should have additional options/behavior in case where input already has annotations

[jsstevenson]

Currently, the VCF annotator errors out if you give it a VCF that has already been annotated. Not sure this is preferred behavior.

This isn't super concrete, but some broad ideas from 2025-06-25 call

• "validator mode" -- walk through the VCF and raise error or log for any cases where the computed ID is different
• "updater mode" -- recompute + write a new VCF (ideally update in place but that may be more difficult). Initial sketch of this in feat: enable recomputation of existing annotations in input VCFs #556