Repair

The repair engine applies only conservative, auditable changes by default:

• trim column names and selected values
• normalize known column aliases when no canonical column conflicts
• replace whitespace in sample IDs with underscores
• lowercase condition labels
• remove fully empty rows
• normalize FASTQ extension case

Every change is written to changes.json.

Suggested repairs are intentionally disabled until the project implements auditable inference rules. Passing --allow-suggestions fails clearly instead of silently applying only safe repairs.