MATLAB source control using Git > (sub)folders

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.