After updating to Intellij 2017.2, building my project creates an /out directory that contains generated source files and resource files. These files duplicate          
        
IntelliJ IDEA is no longer sharing the output with Gradle, please see this ticket for details.
You can either override it via the following configuration:
allprojects {
 apply plugin: 'idea'
 idea {
   module {
     outputDir file('build/classes/main')
     testOutputDir file('build/classes/test')
   }
 }
 if(project.convention.findPlugin(JavaPluginConvention)) {
   // Change the output directory for the main and test source sets back to the old path
   sourceSets.main.output.classesDir = new File(buildDir, "classes/main")
   sourceSets.test.output.classesDir = new File(buildDir, "classes/test")
 }
}
or delegate the build to Gradle: File | Settings | Build, Execution, Deployment | Build Tools | Gradle | Runner => Delegate IDE build/run actions to gradle.