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

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 https://github.com/ga4gh/vrs-python/pull/556