Fix restoring of permissions after a reboot.

It turns out the whole loadedPermissions thing was pointless at this
point, and causing the problem: we would write out the granted
permissions, then at boot load them into loaded permissions, and
never actually put them in granted.

Just remove loadedPermissions.  The grantedPermissions (that is
the permissions the user has approved be granted to the app) are
all we care about.

Change-Id: I54d9dc418d6277ae0b35b8c1fc4b9c11f34f86f0