To make changes to the Roundcube configuration, there are two files to be considered.

This file contains Roundcube default settings. Use this as a reference, but don’t make changes to this file.
/usr/local/topicdesk/roundcube/WebApp/config/defaults.inc.php

To make a change, copy the line(s) from defaults.inc.php and add it to with your change to:
/usr/local/topicdesk/roundcube/WebApp/config/config.inc.php

The config.inc.php file should contain all or your settings, they override the defaults.inc.php settings.