Use Gradle to build the JAR for Android. I might update the build to where you can just use the jar task.
gradle clean cRJ jar
During ndk-build, if you get a permission error regarding libspotify.so in the obj output directory, run this command from the project root directory:
chmod -R 777 *
More info here: https://developer.vuforia.com/forum/android/problem-cygwin