App ops: cleanup, handle root and shell, perms.

Rework how the shell user is defined so that it is
associated with an actual apk, instead of being a free
roaming uid with special permissions assigned to it.
This allows us to correctly account for its operations
in app ops.

Implement a special case for the root user in app ops --
it is always allowed, always with the package name "root".

Add various code to take care of cleaning up package state
from app ops -- when packages are uninstalled, and during
boot if any packages currently being stored no longer exist.

Also fix a bug in the activity manager to correctly grant
permissions in all cases when onNewIntent() is being called.

Change-Id: Iae9f6d793ee48b93518c984ad957e46ae4582581