Gradle/Compile Problem after update to 2016.3 163.6110.12

In my my project I need to support  resources that can be located both in the source dir and the resource dir, so in my build.gradle I have the following:

sourceSets {
    main {
        java {
            srcDirs = ['src/main/java']
        }
        resources {
            srcDirs = ['src/main/java','src/main/resources']
        }
    }
}

I'm not soliciting an opinion on whether this is good practice or not. Suffice it to say I have good reasons for doing it this way. (Putting resources in the source path).

In the previous EAP build this was working (IDEA was marking src/main/java as both a source dir AND a resource dir). In the new EAP build I get NoClassDefFoundError on project build. How do I now configure support for resources on the source path?