I'm currently building a new site using a minimal flat file markdown-embracing CMS called Pico. Once nice thing about flat file systems, of course, is easy deployment. Just grab all your files, push them to any host and you're good to go.
I'm using Git only for keeping track of the codebase and don't want to add content files to the repository. However, it would be tedious to manually keep track of the files added, changed and removed, so I decided to let rsync take care of that.
I found this nice shell script on Codewall