refactor/audit regression baseline

[mtcicero26]

• refactor inference tagging and stabilize test gates
• harden output helpers and share streaming filters
• cover daf call input source checks
• cover daf raw call output parity
• remove unused bam merge helpers
• cover call model resolution
• centralize region bam cat cleanup
• centralize region bam merge fallback
• harden bam sort index wrappers
• extract region bam concat fallback
• type region worker contracts
• share region result aggregation
• cover region worker cleanup failures
• extract fused inference stage helpers
• trim fused recall copy overhead
• speed up daf context encoding
• benchmark daf encoder fast path
• Make ruff lint gate pass
• Report per-read worker failures
• Speed up m6a context encoding
• Reduce Viterbi memory traffic
• Avoid HMM observation copies
• Split mode-specific read encoding
• Freeze HMM logs for inference workers
• Reuse footprint extraction helper
• Speed up footprint run extraction
• Reuse apply tag writer in region workers
• Avoid duplicate footprint state scan
• Close fused DAF reference handle
• Close recall TF BAM handles on failures