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What I do is just keep all of the dotfiles in ~/dotfiles and symlink them to the home directory, then I can keep track of them with git. Doesn't have to be any more work than that. Maybe it's not an issue for me because I only use one machine, and when I switch to another, I just pull down my dotfiles from github and symlink them again. I only do this every couple years.

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This is what I do as well, and I also have a little script that creates all the symlinks in my home directory as well. Dead simple, and it works. I was hoping Stow would somehow be an improvement over that but I don't really see how it does anything more for you.

I agree and think don't understand why you'd want your dotfiles to depend on Make, Ruby/rake, etc. let alone something like Stow. Git and a shell are enough; you can eliminate the Git dependency by packaging from a post-receive hook too.

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