Case 3 alignment (contigs + reads)

[crashfrog]

Parent

#58 (Phase 1 MVP: Evidence-Informed Alignment with Deferred Filtering)

What to build

Extend AlignmentExecutor to support Case 3: M contigs + N reads without reference. Uses centroid contig as coordinate system (selected during plan phase). Aligns M-1 other contigs to centroid, then aligns N reads to centroid. Total: M+N-1 alignment tasks (centroid doesn't align to itself).

This is the key innovation enabling analysis of populations without a reference genome.

Acceptance criteria

• Case 3 detection in AlignmentExecutor (check plan metadata for centroid_id)
• Align contigs to centroid (not to each other)
• Align reads to centroid
• Tests: 3 contigs + 5 reads → 7 alignment tasks (centroid is task 0, doesn't self-align)
• Tests: centroid verified as coordinate system (all target_id == centroid_id in tasks)
• Integration test: plan (case 3) → align all tasks → merge → verify provenance

Blocked by

#78 (alignment executor), #67 (use case detection with centroid)