[codex] Enrich PhaseGroup with assembly metadata

[iskandr]

Summary

• enrich PhaseGroup with assembly-backed cDNA, protein, and transcript metadata
• populate those fields only for protein-sequence-backed phase groups and keep read-only groups conservative
• add regressions showing the direct-neighbor phasing API stays unchanged while the group object becomes richer

Testing

• ./lint.sh
• ./test.sh

Closes #178

[coveralls]

coverage: 93.216% (+0.02%) from 93.194% — codex/phase-group-assembly-support into master