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I use rcm, which is made by the folks at Thoughtbot. It's dead-simple—it just creates symbolic links in place of files. I'd highly recommend it for a simple and quick approach.
I keep all my dotfiles in their usual place and manage them with yadm. It's more or less a wrapper around git, so just point it at your dotfiles and launch a new repo on github to store them. There are more advanced features if you commonly switch between computers too. It will take work to reorganize your files and learn git if you don't know it already, but it's worth it.
I saw a structure like this initially here: https://github.com/WilHall/.dotfiles after reading some of his vim blog posts on the thoughtbot blog.
I use home-manager with Nix. Works really well, and can handle a lot more than just dotfile config, on multiple platforms.
I stumbled upon DotBot. It's a lightweight solution that allows me to structure my dot files in a better way. You are still technically symlinking files and folders from your .dotfiles, or whatever you name it, to other locations, but I do more than that with it.
You are welcome to check out my GitHub Dotfiles Repo.
I have a dotfiles install script that fetches my config git repos & install their dependencies. It's a 126 loc readable bash script, it took me about 30 minutes to write it. I find it nice to have a simple & understandable solution.
Pilgo, a configuration-based dotfiles manager which I created.
Examples in my dotfiles.
I also use a bare repo, but I use dotbare for fzf+git superpowers.
I manage my own dotfiles with gnu stow and git. This combination works on any system and is pretty minimalist.
I wrote an article on this, and also a made a little starter repo that will help you get familiar with how stow works. If you have any questions, feel free to ask!
I'm using make to manage the symlinks and a few other things, with git ofc. (https://github.com/LoricAndre/dotfiles if you wanna check it out)
I use Dotfiler, my very own dotfiles manager!
Chezmoi is the heart of my current setup. I like it because it allows enough customization to easily handle the many OS’s I use - Linux, macOS, BSD’s.
https://github.com/qanuq/mydotfiles all is in the develop branch.
I'm using vcsh which is basically a small wrapper around git. The resulting repository is this in my case.
So I ended up creating my own very simple tool that can do just that (single python script with no dependencies): Dotref
My script don't break often.