I followed the directions at https://doc.owncloud.org/server/10.0/admin_manual/maintenance/manual_upgrade.html for manually upgrading the server
I enabled maintenance mode
I stopped the webserver
I renamed my directory with a -old and unpacked the tar into the /var/www/owncloud directory
I copied over my config and data
I tried to disable the apps and got an error saying my php install (5.5.9) was too old, so I upgraded to php 5.6
now i get all kinds of errors when trying to run any php occ command
I tried changing the owner of the files in /var/www/owncloud to my www-data user with no luck either
example output
sudo -u www-data php occ app:disable activity