It is located in one of the dex files, which contains all classes. You can verify it in AS.
But you should only amend such files before you build, not after.
(The mainActivity in a cordova app does not contain much more than the name of the package and the html file to open really.)
Exactly what are you trying to do?
(If you are trying to release someone elses game by changing the package name, it will not work...)