Pressing Shift+F6 seems only to rename the last directory.
For example, in the project com.example.test it will offer to rename test only. The same applies if I navigate to package name in .java or Manifest file and press Shift+F6.
So is there a way to rename the package?
You can do this:
R.javaclass and the press F6 (Refactor->Move…). It will allow you to move the class to another package, and all references to that class will be updated.