Do you want to ignore them with mix ecto.migrate? Not sure how to do that, but in Ecto.Migrator.run/4 you need to pass a repo to run migrations for, so you can do it there, and it’s what usually gets suggested to be used with releases.
I ran into this same question. It seems you can simply remove MyApp.LegacyRepo from ecto_repos in your config. It will still be usable in your codebase but it will not be used for migrations as that is what the ecto_repos key is mainly used for.