Here's some code that you can use to force certain dependencies to be last in the dependency list.

In this case, we are forcing junit to be last in the list.

import org.gradle.plugins.ide.idea.model.Module
import org.gradle.plugins.ide.idea.model.SingleEntryModuleLibrary

idea.module.iml.whenMerged { Module module ->
    Collection<SingleEntryModuleLibrary> singleEntryModuleLibraries = module.dependencies.findAll { it instanceof SingleEntryModuleLibrary }
    Collection<SingleEntryModuleLibrary> toDemote = singleEntryModuleLibraries.findAll { it.libraryFile.name.startsWith("junit") }
 
    module.dependencies.removeAll(toDemote)
    module.dependencies.addAll(toDemote)
}

I would like to see this fixed, caused us several hours of problems. Running our application from a Gradle build worked, running in IntelliJ build didn't due to weird issues like signed jar security exceptions, etc.

Thanks for the work-around Luke, we're trying that now.

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Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.