gluon-mesh-vpn: fix fastd <-> tunneldigger migration

The generic upgrade script is moved to run after the more specific scripts.
In addition, the script will now remove the configuration sections of
uninstalled VPN packages, so both positive and negative changes of the
default enable state can be migrated correctly.

Based-on-patch-by: Cyrus Fox <cyrus@lambdacore.de>
Fixes: #1187