util/ general utility functions to keep code as compact and as much in one place as possible.services/ service files to interact and maintain stuff.gui/ includes everything related to UI elements.
If you are doing custom modifications to the codebase and have a fork you are on your own for staying up to date with upstream (this repository), google stuff like "merge from upstream" and learn how to use Git. If this is not the case for some reason you'll have to redo the steps in the Making changes to the source code section of the SETUP. CMake should be handling removed / added files automatically without any user input.
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