Along side your Source folder (if you have one), there may be a Plugins folder in your project root. You want to create a folder under Plugins called "CLionSourceCodeAccess", all of the files from the repository should go in there.
Starting your editor up should compile the plugin.
**STOP! Hammer Time! ** If your project does not have any C++ code files in it -- meaning you did not create it from a C++ template, or you haven't added any C++ class files, UE will NOT compile the plugin. You need to add a C++ file from inside of the editor (there is a helper available), then restart UE for it to detect and compile the plugin.
You will then be able to turn it on via the Plugins window.
After you have the plugin turned on, you will need to setup Unreal to use it as a code source accessor. You do this by going into your Editor Preferences and selecting CLion from the list.
The next step is to setup the plugins settings by going to your Project Settings window. Near the bottom is the CLion settings (under Programming).
Most of these settings attempt to automatically set themselves, however the logic is still fuzzy. All that is required currently is the path to the mono executable (when on any platform outside of Windows), and the path to the clion executable.