Eu sei como usar personalizadoAndroid.mk com gradle antigo:

    sourceSets.main {
        jniLibs.srcDir 'src/main/jni'
        jni.srcDirs = [] //disable automatic ndk-build call
    }

    // call regular ndk-build(.cmd) script from app directory
    task ndkBuild(type: Exec) {
        commandLine '/.../android-ndk-r10e/ndk-build', '-C', file('src/main').absolutePath
    }

    tasks.withType(JavaCompile) {
        compileTask -> compileTask.dependsOn ndkBuild
    }

Não está funcionando com o novo gradle:com.android.tools.build:gradle-experimental:0.2.0 :

Error:Cause: com.android.build.gradle.managed.AndroidConfig_Impl