Why does Gradle downgrade my transitive dependencies in a Grails 3.1 application?

The thing causing it is the spring-boot-dependencies-1.3.3.RELEASE.pom

This forcing the flyway version to 3.2.1

According to the Spring Boot docs you should be able to add a line like this to your build.gradle:

ext['flyway.version'] = '4.0.1'