Some recent version seems to have changed the default way IntelliJ compiles Gradle project. It used to be that it still used the IntelliJ build system, which puts resources and classes in one folder. Now "Delegate to gradle" seems to be the default, and gradle puts resources and classes in two separate folders. Make sure to set IntelliJ to not delegate to Gradle (https://www.jetbrains.com/help/idea/work-with-gradle-projects.html#delegate_build_actions).
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