#45464 made db:prepare load the schema instead of running all the migrations if and only if the database is empty. While there is performance benefits, this behavior made it near impossible to test the migrations in CI where you have an ephermal empty database. Since the CI database is empty, all the migrations are skipped. And it might not be possible to run migration down&up in CI since not all migrations are reversible.

I can just replace db:prepare with other manual commands in CI, but it seems to contradict with what db:prepare is designed for.

Is there any recommendations?

BTW, this change also leads to complex problems like #55372 .