[codex] Add explicit phase group objects

[iskandr]

Summary

• add explicit PhaseGroup objects for read-based and protein-sequence-based phasing
• preserve legacy phased_variants_in_* semantics as direct pairwise neighbors
• add regression tests for transitive phase groups and singleton variants

Testing

• ./lint.sh
• ./test.sh

Closes #72

[coveralls]

coverage: 93.194% (+0.08%) from 93.113% — codex/explicit-phase-groups into master