feat: embed reference M5 checksums in BAM headers

[jayhesselberth]

Summary

• Add ref_dict rule in aatrnaseq-reference.smk that runs samtools dict to generate a sequence dictionary with MD5 checksums from the validated reference
• Modify bwa_align in aatrnaseq-process.smk to reheader aligned BAMs, replacing @SQ lines with those from the dict (adding M5 and UR fields) while preserving @HD and @PG lines
• M5 fields propagate automatically to downstream BAMs (inject_ubam_tags → classify_charging → transfer_bam_tags → finalize_bam) since those rules copy headers via pysam

Test plan

• pixi run dry-run — DAG resolves, ref_dict appears before bwa_align
• snakefmt passes
• pixi run test — full test run with test data
• Verify final BAM headers: samtools view -H .tests/outputs/bam/final/test_sample/test_sample.bam | grep '^@SQ' shows M5: and UR: fields

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