Moodle Mobile project has 2 kind of files: development files and release (auto-built) files.
When we develop the app we work using the development files, where each controller/service/directive/whatever has its own file. These files are NOT included in the index.html, they aren't used by the app. When we want these changes to take effect, we "build" the release files (under build/ folder) so the changes made in the development files are reflected in the app. Initially we included these build files in the moodlemobile2 repository, but that caused some integration problems so we finally removed them. In the moodlemobile-phonegapbuild repository these build files are included, so there's no need to manually build them.
That means that if you want this change to take effect in the app you have to apply it to the build JS file. In here: https://github.com/moodlehq/moodlemobile-phonegapbuild/blob/master/build/mm.bundle.js#L4802
I hope I made sense