I looked through the Advanced Topics on Codename One's website but haven't found anything on how to implement instructions for native Android libraries that require adding apply plugin:[plugin name here] to the application's top-level build.gradle file.
Is there a way to do this?
There is no current way of adding a new plugin entry, I've added a new build hint android.gradlePlugin which should be available in the next server update (Friday 29th of September 2017).
You should be able to use it like this (untested):
android.gradlePlugin=apply plugin: 'pluginA';apply plugin: 'pluginB';