Fix issue #2154794: Force close when start facebook application.

I think when we were scanning the updated app in the system image,
from an older version on the data partition, we were not setting
the existing package to have the system flag, so not auto-granting
any new permissions.

This also includes some other cleanup in the package manager to
remove old files in various places, and tighten up logging.

Also similar logging cleanup elsewhere.

Change-Id: I6d113c7cf7e736ab9be512d6d7c94c806a24199a