First off, love this app, keep up the awesome work.
Secondly, what do you think about adding XDG support? The global config file would then be $XDG_CONFIG_HOME/github-todos/github-todos.cfg (or similar). The default (if $XDG_CONFIG_HOME is not set) would be ~/.config/github-todos/github-todos.cfg in addition to/instead of ~/.github-todos. Or let the user specify a custom location via an environment variable like GITHUB_TODOS_CONFIG or something.