This repo started out with just my . files (mainly vim files), but over time I’ve added to it, and now it represents a subset of all my command-line folders.
I store all my command-line files in a folder (cl), then under that folder there are 3 sub-folders (cl/bin cl/etc cl/doc), to keep them organized away from all my other files. I link (etc/link) the dot files to the root of my home folder, so I prefer to store them without the . (gitignore rather than .gitignore), then I add the dot in the link. So if you use one, make sure you put the dot back.
I mod these all the time, and sometimes I break stuff. Also, my main platforms are OS X and Linux (Debian based) in the console, not XWindows. Most of my stuff works just fine in something like gnome-terminal, but I usually only check my main platforms when I make changes.