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Isovar phase resolver: RNA-assembly evidence for effect prediction (#269) (#351)

Adds the first piece of #269: an IsovarAssemblyProvider protocol and
an IsovarPhaseResolver concrete class that plug into
Variant.effects() / VariantCollection.effects() via a new
phase_resolver= kwarg. When the resolver has an assembled contig
covering (variant, transcript), the returned effect's
mutant_transcript slot is populated with the contig-derived
MutantTranscript — the attached protein is the protein actually
observed in RNA, not one inferred from reference + edits.

Varcode deliberately does not import Isovar. The provider interface
is three duck-typed methods (has_contig, variants_in_contig,
mutant_transcript) that Isovar or any contig-based tool can satisfy.
Long-read haplotype callers, custom assemblers, or test stubs all
plug in the same way.

IsovarPhaseResolver.in_cis answers the basic phase question — two
variants are cis if they appear on the same contig, trans if on
different contigs, None when no evidence either way. One-sided
evidence is handled (v1 without its own contig but present in v2's
contig variants → cis).

New:
- varcode/phasing.py — IsovarAssemblyProvider (runtime-checkable
  Protocol), IsovarPhaseResolver, apply_phase_resolver_to_effects
  helper.
- mutant_transcript attribute on MutationEffect base class
  (class-level None default) so every effect kind has a natural
  slot for an attached assembly, not just SV and splice effects.
- phase_resolver= kwarg threaded through Variant.effects and
  VariantCollection.effects.
- tests/test_isovar_phase_resolver.py — 13 tests exercising the
  contract with an in-memory StubAssemblyProvider; no Isovar
  dependency.

Out of scope (future PRs in the #269 staging):
- HaplotypeEffect class for joint cis-variant effect prediction
- DNA PS-tag resolver (VCFPhaseResolver)
- Read-co-occurrence resolver (RNAReadPhaseResolver)
- Unphased-proximity candidates (cis/trans possibility set)
Source Files on build 24754840625
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