My problem was strange and took some time to find. Somehow the package of the src file changed so that the last entry in the package was deleted. So for example initially my class MyActivity.java was in package com.abc.client.test.app but after I added a user permission, the app got removed and the package was renamed to com.abc.client.test. I don't know how it happened. Renaming the package and putting the java file in the correct place fixed the problem.
