Intellij dependencies not appearing with custom configuration

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Each module in IDEA has basically two kinds of sources - production and test. There are a few classpath scopes controlling how sources and dependencies are used together when project is built and run. Gradle by default maps main and test sourceSets and related configurations to IDEA projects/modules.

Now if you want to add another sourceSet + configurations for your additional code you will need to customize the mapping between Gradle and IDEA.Take a look at the documentation - most interesting for you is http://www.gradle.org/docs/current/dsl/org.gradle.plugins.ide.idea.model.IdeaModule.html

You will want something like

idea {
  module {
    scopes.TEST.plus = configurations.apiFunctionalTestCompile
  }
}