fix: validate reference allele stated in HGVS expressions

[developer-rpai]

Summary

Closes #364.

HGVS-to-VRS translation silently accepted an incorrect reference allele: NM_006087.3:c.900C>A produced a plausible-looking VRS Allele even though the true reference base is G (per the ClinGen Allele Registry: "IncorrectReferenceAllele ... given=C, found=G", independently confirmed against NCBI RefSeq: with the CDS annotated at 373..1707, c.900 maps to n.1272, and NM_006087.3 n.1272 is G).

Root cause

The HGVS parser preserves the stated reference allele (sv.posedit.edit.ref), but HgvsTools.extract_allele_values() never inspected it, so a wrong reference flowed straight into the emitted Allele. The gnomAD translator path already validated reference alleles via DataProxy.validate_ref_seq(); the HGVS path did not.

Change

• HgvsTools.extract_allele_values() accepts require_validation: bool = True. After any c.->n. mapping, when the HGVS expression states a reference allele (e.g. the C in c.900C>A, or deleted bases in g.44908822delC), it is validated against the reference sequence, raising DataProxyValidationError on mismatch; with require_validation=False the mismatch is only logged.
• AlleleTranslator._from_hgvs() passes require_validation through, so the existing translate_from(..., require_validation=False) escape hatch now applies to HGVS input too.
• Default behavior: refuse to emit an invalid Allele. Edits that state no reference allele (insertions, duplications, bare deletions) skip validation entirely.

Tests

• New hermetic regression tests in tests/extras/test_allele_translator.py (no UTA/seqrepo network needed): the exact issue variant raises by default; a del-with-ref mismatch raises; correct-reference controls (substitution and deletion-with-ref) still translate; require_validation=False returns the allele with a logged warning; edits without a stated ref skip validation.
• Negative control: with the src/ fix reverted, the two "raises" tests fail (pristine code emits the Allele); with the fix, all 5 pass.
• Added the VCR cassette interactions required by the new reference lookups in test_from_hgvs and the test_hgvs substitution cases. Ground truth for the added interactions was cross-checked against the repo's own previously recorded cassettes and NCBI RefSeq.
• Ruff check and format --check pass on all touched files.

Limitations

• The UTA-backed VCR tests (test_from_hgvs, test_hgvs) could not be executed in this environment (no UTA or seqrepo access). Cassette completeness was verified by replaying the fixed code path against the recorded cassettes with the session-scoped cache shared, but CI is the authoritative check.
• 3 pre-existing test_vrs_normalize.py failures (VCR cassette mismatches) occur identically with and without this change.

Related: #151 (maintainer discussion supports validating supplied reference alleles and raising rather than emitting invalid objects).