As of the latest ISO 0.4.5, the Upgrade feature has been included.
Installing ISO 0.4.5
The following actions must be executed to restore proper permissions for usability that have not been yet automated. As 'root':
chown -R mc:games /usr/games/minecraft chown -R mc:games /var/www chown -R root:root /var/www/hiawatha/admin/cgi-bin chown mc:games /var/www/hiawatha/admin/cgi-bin
All releases since 0.4.6 now contain a script /root/runonce/fix_permissions that can execute these commands if permissions ever need to be restored.
Upon all Upgrades
Part of upgrading packages re-inserts files that are missing or may have been removed (even deliberately). One such file is /var/www/hiawatha/index.html. This is the default landing page for hiawatha webserver, but its presence will prevent the DIRECTORY LISTING you may be familiar with by visiting your IP address in the browser. This file may be safely deleted (or kept)--/snapshots and /admin will still be accessible