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varcode.transforms + pair_breakends (#364, planning + scaffold) (#367)

* Scaffold varcode.transforms with pair_breakends signature (#364)

Planning PR — implementation tracked in the description. This commit
adds only the minimal structural pieces so reviewers can see the
shape:

* Variant.source_variants attribute (default ()), populated by
  transforms to record provenance.
* varcode/transforms package with pair_breakends signature, full
  docstring spelling out the pairing rules, edge cases, and metadata
  merge contract. Body raises NotImplementedError pointing at #364.

* Implement pair_breakends transform (#364)

Walks the VariantCollection, builds a transient MATEID/PARID -> variant
index from the captured source row IDs, and replaces each symmetric
pair of BND rows with a single combined StructuralVariant. The
combined row carries both endpoints (start + mate_start), source
variants tuple for provenance, and a merged metadata entry per source
path.

Behavior:
- Pass-through for non-BND variants, single-row TRA, single-ended
  BNDs (no MATEID), already-paired inputs (source_variants non-empty
  -> idempotent).
- Warnings for: mate ID missing from VC, asymmetric MATEID, N-way
  collisions (>=3 rows share an ID group).
- Raises on per-sample GT disagreement — caller bugs surface instead
  of being silently coerced.
- alt_assembly: lex-A wins on conflict (deterministic).
- FILTER: union of tokens; stricter wins (PASS drops out when any
  half has a non-PASS label).
- qual: min(A, B) when both present.
- info: A's values win; key dropped if both are MATEID/PARID.

The SV annotator's existing per-(variant, transcript) dispatch
consumes combined rows transparently — _coding_transcript_at already
reads mate_contig/mate_start, which combined rows populate. No
annotator code changes required; the reverse-complement warning now
fires once per combined variant instead of once per half.

* Test matrix for pair_breakends + PARID alias in parser (#364)

* 1... (continued)
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