I discovered the following tinkering with a client's CC 4.0 box:
1. system-mysqld is used by ClarkConnect's reporting infrastructure -- eg. web proxy reports.
2. system-mysqld stores data in /var/lib/system-mysql, and the configuration file is /usr/share/system-mysql/etc/my.cnf
3. You need to use chkconfig to have the mysql daemon start up automatically each time you start. However, in ClarkConnect you can use the web management interface to do this for you: https://domain.tld:81/
4. The my.cnf you checked was for the 'user-level' mysql daemon, which stores data in /var/lib/mysql. You can install phpMyAdmin to the web root and access it (ensure web server is installed and running) using http://127.0.0.1/phpMyAdmin or so. You should be able to use 'root' with no password in config.inc.php (remember to add a user and change password later).
