Check permission via PermissionManagerService in PackageManagerService.

As the first step towards moving PermissionsState out of package
Setting. The usages for GIDs and installing a system package after
uninstalling its update will be addressed in another change.

Bug: 158736025
Test: presubmit
Test: System boots
Change-Id: Ic45a97eabb6957836d691ac1d3c9092648b0b523