The reason files with numbers with different changes are kept is because when there are more than a handful of devs working on the same schema, who has the right magic 1 step "Dev schema"?

Your migration tool is bad and you should feel bad.

Schema changes aren't hard. It's the mismatch of devs knowing how big a table is in production + the downtime caused by a data migration that is the hard problem. Data retention, partitioning, and other data archiving things are rarely the top of mind for apps until it's usually too late and "hard".