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Alternatively, if you are setting up CLion on a Ubuntu/Debian machine (this may work for OSX as well), you can put your
source /opt/ros/{your_ros_distro}/setup.bash
in the ~/.profile (or /etc/profile for system-wide environment setup). This way all logins environments (interactive/non-interactive/graphical) will be populated with the ROS environment variables and it will not matter whether you start CLion from the terminal or the application launcher.
One gotcha however is if ~/.bash_profile exists. In that case, place the setup.bash setup script in the ~/.bash_profile script or modify the ~/.bash_profile script to source the ~./profile script.
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