Gradle flavors for android with custom source sets - what should the gradle files look like?

I've got an old eclipse project I've moved into android studio and setup to use flavors. It seemed to be working fine till I started trying to use different java files between my flavors.

My project setup is this:

ProjectRoot
+- acitonbarsherlock
+- facebook
+- myLib1
+- myProject
   +- src
      +- commonFiles
         +- flavor1
         +- flavor2
   +- res
      +- flavor1
      +- flavor2

The innards of the myProject gradle file android closure looks like this:

android {
compileSdkVersion 17
buildToolsVersion "18.0.1"

signingConfigs {
     ...
}

productFlavors {
    flavor2 {
    }
    flavor1 {
    }
}

sourceSets{
    main {
        manifest.srcFile 'AndroidManifest.xml'
        java.srcDirs = ['src/commonFiles/java']
        resources.srcDirs = ['src/commonFiles/java']
        aidl.srcDirs = ['src/commonFiles/java']
        renderscript.srcDirs = ['src/commonFiles/java']
        res.srcDirs = ['res']
        assets.srcDirs = ['assets']
    }

    flavor2 {
        manifest.srcFile 'AndroidManifest-flavor2.xml'
        res.srcDirs = ['res-flavor2', 'res']
        java.srcDirs = ['src/flavor2/java','src/commonFiles/java']
        resources.srcDirs = ['src/flavor2/java','src/commonFiles/java']
        aidl.srcDirs = ['src/flavor2/java','src/commonFiles/java']
        renderscript.srcDirs = ['src/flavor2/java','src/commonFiles/java']
    }

    flavor1 {
        manifest.srcFile 'AndroidManifest.xml'
        java.srcDirs = ['src/flavor1/java','src/commonFiles/java']
        resources.srcDirs = ['src/flavor1/java','src/commonFiles/java']
        aidl.srcDirs = ['src/flavor1/java','src/commonFiles/java']
        renderscript.srcDirs = ['src/flavor1/java','src/commonFiles/java']
        res.srcDirs = ['res-flavor1','res']
        assets.srcDirs = ['assets']
    }

    // Move the tests to tests/java, tests/res, etc...
    instrumentTest.setRoot('tests')

    // Move the build types to build-types/<type>
    // For instance, build-types/debug/java, build-types/debug/AndroidManifest.xml, ...
    // This moves them out of them default location under src/<type>/... which would
    // conflict with src/ being used by the main source set.
    // Adding new build types or product flavors should be accompanied
    // by a similar customization.
    debug.setRoot('build-types/debug')
    release.setRoot('build-types/release')

}

buildTypes {
    release {
        signingConfig signingConfigs.release
    }
}

}

With my setup like this gradle complains about not being able to find classes I'm trying to inherit from commonFiles in flavor1 or flavor2.

From the various other topics I've looked at on here I see others not even defining source sets, and I feel like what I'm doing in them is perhaps too much.

Has anyone experimented with this before and know how this should properly be configured?

I think you'd be better off not defining custom sourceSets but using the default gradle configuration. I used to do custom sourcesets until I realized the conventions are, well, convenient.

You'll want something like this:

+ src
    + main // this is your common code
        + java 
        + res
    + flavor1
        + java
        + res
    + flavor2
        + java
        + res

Then you can just go ahead and remove the sourcesets closure from your build.gradle

NOTE: For the gradle configuration, resources are merged or overridden whereas all java code is put on the same class-path. For example, the AndroidManifest.xml files for each flavor need only have the differences from main's manifest file. Having an asset, for example, ic_launcher in a flavor overrides the ic_launcher from main if such file exists. However, having a file HomeActivity.java in both main and the flavor is not possible and will give a duplicate file error.