Android : android studio 1.0 + ndk how to use custom makefiles

Just migrated from eclipse to android studio but ndk compilation is really a pain. How can I use my custom makefile to compile my jni libraries using android studio? I tried to make a gradle task for that purpose. Check out my gradle file:

apply plugin: 'com.android.application'

android {
    compileSdkVersion 21
    buildToolsVersion "21.1.2"

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

    defaultConfig {
        applicationId "com.example.exampleApp"
        minSdkVersion 9
        targetSdkVersion 21
        compileOptions {
            sourceCompatibility JavaVersion.VERSION_1_7
            targetCompatibility JavaVersion.VERSION_1_7
        }

        ndk {
            moduleName "nativeLib"
        }
    }

    buildTypes {
        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.txt'
        }
    }
}

dependencies {
    compile project(':smoothProgressBarLib')
    compile 'com.android.support:appcompat-v7:21.0.3'
    compile 'com.google.android.gms:play-services:+'
    compile files('libs/dexguard_util.jar')
}

task buildNative(type: Exec) {
    Properties properties = new Properties()
    properties.load(project.rootProject.file('local.properties').newDataInputStream())
    def ndkDir = properties.getProperty('ndk.dir')
    def ndkBuild = ndkDir + File.separator + "ndk-build.cmd";
    def ndkBuildingDir = new File("src/main");

    commandLine ndkBuild, '-C', ndkBuildingDir.absolutePath
}
tasks.withType(JavaCompile) { compileTask -> compileTask.dependsOn buildNative }

But I get the following error on windows 8.1

Process 'command 'C:\Users\Thanos\android-ndk-r10d\ndk-build.cmd'' finished with non-zero exit value 2

Any ideas what Am I doing wrong? It's driving me crazy