feat: Warn if samples are missing in FASTA

[gp201]

Only print per-sample missing warnings when debug=True. By default print a summary warning.

[Copilot]

Pull request overview

This PR modifies the warning behavior for missing samples in process_and_reroot_lineages. Previously, a per-sample warning was always printed for each sample not found in the FASTA file. Now, per-sample warnings are only shown when debug=True, and a summary warning (showing count and percentage) is always displayed when any samples are missing.

Changes:

• Gate per-sample "not found in FASTA" warnings behind the debug flag, and add a summary warning showing the count/percentage of missing samples
• Update the existing test to verify the new summary warning and confirm per-sample warnings are suppressed when debug=False
• Add two new tests: one verifying per-sample warnings appear with debug=True, and one confirming the summary warning fires for any number of missing samples

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
barcodeforge/ref_muts.py	Track missing_count, gate per-sample warnings behind debug, add summary warning with count and percentage
tests/test_ref_muts.py	Update existing test assertions for summary warning; add test_..._debug_shows_per_sample_warning and test_..._summary_warning_any_missing tests

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