I keep all my dotfiles in a git repo (github.com/gonsie/dotfiles). The readme there has some details, but at a high level: I download the repo and keep that separate from my 'installed' dot files. I use a synch.sh script to synchronize the repo with what is installed and I use git to synchronize across machines. The synch script has some smarts and knows how to set up a new machine, otherwise, it diff's the repo and installed files to figure out what I've changed.
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