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
a33e3f7925