Each time some arbitrary package was installed using dpkg or apt-get, the update notification in Qubes VM Manager was cleared.
No matter if there were still updates pending. (Could happen even after the user running `apt-get dist-upgrade` in case of package manager issues.)
No longer clear upgrade notification in QVMM on arbitrary package installation.
Check if upgrades have been actually installed before clearing the notifications.
https://github.com/QubesOS/qubes-issues/issues/1066#issuecomment-150044906
