You could customize oc design without hacking core files.
A good point to start is to copy the example theme folder and rename it to whatever you want.
then you have to edit the /owncloud/config/config.php file and add your theme here
'theme' => 'customtheme',
Also please have a look into the manual for further informations and examples
Available config.pgp parameters: https://doc.owncloud.org/server/9.1/admin_manual/configuration_server/config_sample_php_parameters.html
BTW: OC switch theme back to core after updating to prevent (possible) inconsistent functionality with custom themes ( things might change, its an update ). All you have to do is to edit the config.php to set your custom theme again.