Hi harderthan,
I confirm you that using my plugin you no longer need to run clion from a terminal. 
You can simply import a new ROS workspace and it will set in CLion all the environment variables in order to allow the IDE to understand how to find all the depencencies.
Basically, you have to configure the available ROS versions if they aren’t in /opt/ros and when every time you will import a ROS workspace, it Idetects the right ROS version to use by the CMakeLists.txt link in the src folder and then he set the right environment variables for the cmake configuration. In this way CLion will use the right environment variable every time.
Regards,
Paolo