build gradle with ndk build tasks that are using an alternative configuration or Application.mk for debug builds, using the new model.

build.gradle

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

apply plugin: 'com.android.model.application'

model {
    android {
        compileSdkVersion = rootProject.ext.compileSdkVersion
        buildToolsVersion = rootProject.ext.buildToolsVersion

        defaultConfig.with {
            minSdkVersion.apiLevel = 14
            targetSdkVersion.apiLevel = 23
        }
    }

    android.ndk { // keeping it to make symbols look up happy.
        moduleName = "mymodule"
        ldLibs += ['log']
        cppFlags += "-std=c++11"
        cppFlags += "-fexceptions"
        cppFlags += "-I${file("src/main/jni/prebuilts/include")}".toString()
        stl = 'gnustl_shared'
        platformVersion = 15
    }

    android.sources {
        main.jni {
            source {
                srcDirs = ['src/main/none']
            }
        }
        main.jniLibs {
            source {
                srcDirs = ['src/main/libs']
            }
        }
    }
}

// call regular ndk-build(.cmd) script from app directory, in either debug or release mode
tasks.withType(JavaCompile) {
    compileTask ->
        def tmpFile = file('src/main/jni/.debugbuild.tmp') //used to persist the last build type, to avoid triggering rebuilds all the time.
        def ndkBuildExt = Os.isFamily(Os.FAMILY_WINDOWS) ? ".cmd" : ""

        def debugMode = compileTask.name.contains("Debug")
        def taskName = "ndk${debugMode ? "Debug" : "Release"}Build"

        def extraParameter = debugMode ? "NDK_DEBUG=1" : "" // other possibility for debug build:
                                                            // referencing an other Application.mk that contains APP_OPTIM:=debug and other options
                                                            // -> "NDK_APPLICATION_MK=" + file('src/main/jni/Application-debug.mk').absolutePath

        def task = tasks.findByPath(taskName);
        if (task == null) {
             task = tasks.create(name: taskName) { //create ndkReleaseBuild and ndkDebugBuild tasks
                doLast {
                    exec { //execute all this block when the task is executed. (A Build task gets only the commandLine to be executed, so here we're using doLast.exec instead)
                        def rebuildFlag = ""

                        if (!tmpFile.exists()) tmpFile.createNewFile()

                        if (tmpFile.text != String.valueOf(debugMode)) {
                            rebuildFlag = "-B" //ndk build type has changed, triggering full rebuild.
                        }

                        commandLine "ndk-build${ndkBuildExt}", rebuildFlag, '-C', file('src/main').absolutePath, extraParameter

                        tmpFile.write(String.valueOf(debugMode))
                    }
                }
            }
        }
        compileTask.dependsOn task
}

dependencies {
    compile fileTree(dir: 'libs', include: ['*.jar'])
    compile 'com.android.support:support-annotations:23.0.1'
}