I have found that managing dotfiles is not enough. The dotfiles serve no purpose without the software that uses them. My method is to write small scripts, I call them setuplets, that install the software and then symlink the dotfile to its master that I manage in git. In the simplest case, it is just a two line script in a directory, but I have one for each program, and a tool to select which I run when setting up a new linux machine. The more complex ones may install a number of tools and set up environment variables etc. For environment variables, the script drops a script file in a directory, where my bashrc sources it.