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Intron retention with genomic_sequence provider (#296) (#349)

enumerate_splice_outcomes now accepts an optional
genomic_sequence callable: (contig, start_1based_inclusive,
end_1based_inclusive) -> str that returns forward-strand genomic
bases. When present, the INTRON_RETENTION candidate materializes
a real MutantTranscript by inserting the retained intron's cDNA at
the exon boundary and translating from the canonical CDS start —
the premature stop almost always lies within the retained intron,
yielding a truncated mutant_protein_sequence that
classify_from_protein_diff routes to FrameShift / PrematureStop as
appropriate.

- _adjacent_intron_coords helper resolves the intron's genomic
  coords relative to a disrupted exon, handling forward + reverse
  strand transcripts.
- _build_intron_retention_mutant_transcript constructs the
  transcript-order cDNA, reverse-complementing the provider's
  forward-strand bases when the transcript is on the minus strand.
- _splice_side_for_effect keys donor/acceptor off the effect class
  (SpliceDonor, SpliceAcceptor, IntronicSpliceSite via existing
  _intronic_splice_side_is_acceptor, ExonicSpliceSite defaults to
  donor).
- No provider → pre-#296 stub behavior preserved (coding_effect
  None, predicted_class_name "PrematureStop").
- Provider exceptions (missing FASTA, unknown contig) fall back
  silently to the stub instead of propagating.

Cryptic-donor / cryptic-acceptor candidates remain stubs — their
genomic-FASTA integration is a follow-up (needs motif scanning
over flanking sequence).

Tests: synthetic provider exercises the full pipeline; raises
smoke test; back-compat (no provider) unchanged.
Source Files on build 24734718828
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