How to write your thesis in markdown with Github

I'm currently writing my thesis at Haaga-Helia University of Applied Sciences. I want to write with my favorite text editor and with markdown so I can't really write to the schools word template. Writing with markdown makes your life much easier because you never have to think about formatting.

There is one challenge. The final document should be in the official Haaga-Helia format. I made instructions how to convert the file automatically to the Haaga-Helia template: md2HH