Look, this will make the git history look funny, but trimming unnecessary depth from the source tree is a very necessary sanity-preserving measure when dealing with a super-modularized codebase like this one.
While it makes the project configuration a bit less conventional, it will save you several clicks every time you jump between modules. Which you'll do a lot, because it's *modul*ar. The src/main/java convention makes a lot of sense for a non-modular project though. This ain't that.
Several tests were manually running migrations in a large copy-paste blob of code. This makes the test less useful as it's possible to break the code while keeping the tests green by introducing a new migration that never gets run in the tests, and it's also difficult to reason about what the tests are doing.
A new test helper library is introduced with a TestMigrationLoader that can both run Flyway migrations, or load specific migrations in the cases a specific set of migrations need to be loaded. Existing tests are migrated to use the new code.