gradle
В том числе родной источник - экспериментальный

параметры

Базовая конфигурация JNI Gradle

root: build.gradle

buildscript {
    repositories {
        jcenter()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle-experimental:0.8.0-alpha4'
    }
}

allprojects {
    repositories {
        jcenter()
    }
}

app: build.gradle

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

dependencies {
    compile "com.android.support:support-v4:23.3.0"
    compile fileTree(dir: 'libs', include: '*.jar')
}

model {
    android {
        compileSdkVersion = 23
        buildToolsVersion = '23.0.3'

        defaultConfig {
            applicationId = 'com.example.hello'
            minSdkVersion.apiLevel = 9
            targetSdkVersion.apiLevel = 23

            buildConfigFields {
                create() {
                    type "int"
                    name "VALUE"
                    value "1"
                }
            }
        }

        ndk {
            platformVersion = 9
            moduleName "hello"

            toolchain "clang"

            stl "gnustl_static"
            CFlags.add("-DANDROID_NDK")
            cppFlags.add("-std=c++11")

            ldLibs.add("android")
            ldLibs.add("dl")
            ldLibs.add("log")
        }

        sources {
            main {
                jni {
                    exportedHeaders {
                        srcDirs "../../common/headers"
                    }
                    source {
                        srcDirs "../../common/src"
                    }
                }
            }
        }
    }
}

Использование готовых библиотек и OpenGL ES 2.0

root: build.gradle

buildscript {
    repositories {
        jcenter()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle-experimental:0.8.0-alpha4'
    }
}

allprojects {
    repositories {
        jcenter()
    }
}

app: build.gradle

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

dependencies {
    compile "com.android.support:support-v4:23.3.0"
    compile fileTree(dir: 'libs', include: '*.jar')
}

model {
    android {
        compileSdkVersion = 23
        buildToolsVersion = '23.0.3'

        defaultConfig {
            applicationId = 'com.example.glworld'
            minSdkVersion.apiLevel = 9
            targetSdkVersion.apiLevel = 23

            buildConfigFields {
                create() {
                    type "int"
                    name "VALUE"
                    value "1"
                }
            }
        }

        buildTypes {
            release {
                minifyEnabled = false
                proguardFiles.add(file('proguard-rules.txt'))
            }
        }

        ndk {
            platformVersion = 9
            moduleName "glworld"

            toolchain "clang"

            stl "gnustl_static"
            CFlags.add("-DANDROID_NDK")
            CFlags.add("-DDISABLE_IMPORTGL")
            CFlags.add("-DFT2_BUILD_LIBRARY=1")
            cppFlags.add("-std=c++11")

            ldLibs.add("EGL")
            ldLibs.add("android")
            ldLibs.add("GLESv2")
            ldLibs.add("dl")
            ldLibs.add("log")
        }

        sources {
            main {
                jni {
                    dependencies {
                        library "freetype2" linkage "shared"
                    }
                    exportedHeaders {
                        srcDirs "../../common/headers"
                    }
                    source {
                        srcDirs "../../common/src"
                    }
                }
            }
        }
    }

    repositories {
        prebuilt(PrebuiltLibraries) {
            freetype2 {
                headers.srcDir "../../common/freetype2-android/include"
                binaries.withType(SharedLibraryBinary) {
                    def localLib = "../../common/freetype2-android/Android/libs"
                    sharedLibraryFile =
                            file("$localLib/${targetPlatform.getName()}/libfreetype2.so")
                }
            }
        }
    }
}

// The next tasks compile a freetype library using a make file.
// These `.so`'s are then used as the shared libraries compiled above.
tasks.withType(JavaCompile) {
    compileTask -> compileTask.dependsOn buildNative
}

// Call regular ndk-build (.cmd) script from the app directory
task buildNative(type: Exec) {
    def ndkDir = "/Development/android-sdk-macosx/ndk-bundle"
    commandLine "$ndkDir/ndk-build",
            '-C',
            file('../../common/freetype2-android/Android/jni').absolutePath
}

task cleanNative(type: Exec) {
    def ndkDir = "/Development/android-sdk-macosx/ndk-bundle"
    commandLine "$ndkDir/ndk-build",
            '-C',
            file('../../common/freetype2-android/Android/jni').absolutePath,
            "clean"
}

clean.dependsOn cleanNative