MATLAB source control using Git > (sub)folders

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MM
MM 2019-5-29
I've installed and setup Git for my MATLAB/Simulink project using this guide:
http://www.datatool.com/downloads/MATLAB_Source_Control_With_Git.pdf
But I read that git isn't made to work with folders. But my project works with different output and input gathered in different (sub)folders. Will this cause problems? And also when I want to add a folder with a lot of subfolder and files, how can I add this easily to the git? I now had to add every file seperately per folder.

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