I think you are mistaking PCB footprints with Schematic symbols. What is at that github repository are footprints which are .kicad_mod files. These are the correct files for the PCB footprints, and each footprint library is a .pretty folder containing .kicad_mod files. The schematic symbols are a separate library format consisting of .lib files in addition to .dcm files for each library. (The reason why there is such a big difference between the way symbol and footprint libraries are organized is KiCad is changing to a new format. The footprint libraries were done first, and issues hammered out there. The symbols will be changed next.)
For more details, please see the following FAQ entry: