Merge the contents of the mods and assets folders with your own. If you were prompted to overwrite any files, make sure you don't have any of these mods already installed - installing the modified mods on top will not work, as some files need to be deleted.
The (optional) pre-configured settings folder contains configuration settings that I'm currently using, if you don't feel like customizing them yourself, or want to use it as baseline. Hotkey to open HoloUI settings has been movbed to F2.