pm: remove stale permissions

Remove all previously declared permissions of an app, that currently aren't defined in
is actual version. Only remove a permission when:

1.- The app is not the system app
2.- The permission is a normal permission (ignore dynamic and builtin ones, and hence
       permissions derived from a permission-tree)
3.- The permission isn't currently declared by the app
4.- Do not apply if the PackageManager is running in "onlyCore" mode

Change-Id: Ie42a13bd94f0689570426ed06244b31d1213c1aa
JIRA: CML-125
Signed-off-by: Jorge Ruesga <jorge@ruesga.com>