phraya merge CLI

[crashfrog]

Parent

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

What to build

Implement `phraya merge` CLI command in phraya-cli. Reads multiple .phraya files, calls merge operation, writes merged .phraya output. Useful for combining alignment results from multiple samples before filtering.

Query indices (.phraya.queries) remain as separate per-sample sidecars and are not merged.

Acceptance criteria

• `phraya merge <input1.phraya> <input2.phraya> ... --output <merged.phraya>`
• Read all input .phraya files
• Call merge_phraya
• Write merged .phraya file
• Log merge progress to stderr (e.g., "Merging 3 samples...")
• Return non-zero exit code on error
• Integration test: align 2 samples → merge → verify provenance preserved
• Integration test: merged coverage = sum of individual coverages

Blocked by

#79 (merge operation)

[crashfrog]

Resolved by #108