How to use my own Android.mk file with Android Sud

I am defining some variables within the Android.mk file (I am passing some flags for the compiler), but every time I build my project, the Android.mk is overwritten. I am assuming that Gradle is responsible and that I should be looking there? How do I use my own Android.mk file?

Background Info:

Ubuntu 64bit, Android Studio 1.0.1, JDK7. I have wrapped my NDK version with O-LLVM NDK, and as such am editing the Android.mk file located at app/build/intermediates/ndk/debug (it's the only Android.mk file within my project dir), different to the location that the doc for O-LLVM gives examples of.

Also, there is no Application.mk file, so again I am assuming that Gradle is responsible for the calls to the compiler?

Any help would be greatly appreciated.

Kyle

Updated information

build.gradle - (app)

//The following code until the "----" line is the new build.gradle config file
// that disables automatic Android.mk file generation

import org.apache.tools.ant.taskdefs.condition.Os
apply plugin: 'com.android.application'

android {

    compileSdkVersion 21
    buildToolsVersion "21.1.2"

    defaultConfig {
        applicationId "com.md.helloworld"
        minSdkVersion 15
        targetSdkVersion 21
        versionCode 1
        versionName "1.0"
        ndk {
            moduleName "MyLib"
        }
    }

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

    sourceSets.main {
        jniLibs.srcDir 'src/main/libs' //set libs as .so's location instead of jni
        jni.srcDirs = [] //disable automatic ndk-build call with auto-generated Android.mk file
    }

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

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

dependencies {
    compile fileTree(dir: 'libs', include: ['*.jar'])
    compile 'com.android.support:appcompat-v7:21.0.3'
}

/*
//The following code is the original Android.mk file

apply plugin: 'com.android.application'

android {
    compileSdkVersion 21
    buildToolsVersion "21.1.2"

    defaultConfig {
        applicationId "com.md.helloworld"
        minSdkVersion 15
        targetSdkVersion 21
        versionCode 1
        versionName "1.0"
        //The only modified line
        ndk {
            moduleName "MyLib"
        }
    }
    buildTypes {
        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
        }
    }
}

dependencies {
    compile fileTree(dir: 'libs', include: ['*.jar'])
    compile 'com.android.support:appcompat-v7:21.0.3'
}
*/

Android.mk

LOCAL_PATH := $(call my-dir)

include $(CLEAR_VARS)

LOCAL_MODULE    := helloWorld
LOCAL_SRC_FILES := main.c

LOCAL_LDLIBS := -static

include $(BUILD_EXECUTABLE)

Application.mk

LOCAL_PATH := $(call my-dir)

include $(CLEAR_VARS)

APP_ABI := armeabi

NDK_TOOLCHAIN_VERSION := clang3.4-obfuscator

include $(BUILD_EXECUTABLE)

Please note: I am not passing any cflags just yet, I am trying to get a Vanilla build working first

yes, by default the gradle android plugin regenerates and uses its own Android.mk file to compile your sources.

You can deactivate this and use your own Android.mk file instead, by setting this inside your build.gradle configuration file:

import org.apache.tools.ant.taskdefs.condition.Os
...     
android {
    ...

    sourceSets.main {
        jniLibs.srcDir 'src/main/libs' //set libs as .so's location instead of jniLibs
        jni.srcDirs = [] //disable automatic ndk-build call with auto-generated Android.mk
    }

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

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

Note that if you only need to pass your own cflags to the auto-generated Makefile, you can set these inside the cFlags "" property to set inside android { ndk {}}