Check permissions only against packagesettings

Prior to this change there was a chance that an updating app would not
exist in mPackages and cause a permission check for that app to fail.
This change moves all permission checks to use mSettings and the cached
package it contains to do the checks.

Change-Id: I0717bddbb08b1d0dbab3ea79fa0d2067aa858753
Fixes: 76228188
Test: Manual - system starts, permission checks work before / after update