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It depends on what applications you use. I use a twm (i3 and Qtile), neovim is my editor of choice, calcurse my calendar app... And so on. Plus all bash and tty config, and a few other things... https://github.com/mhsalvor/dotfiles
I'm currently happy with yadm. It basically does the same thing, and has some extra features some might find useful. I used just git before and then chezmoi for a while.
I dont believe there is "a best way", since requirements for dotfiles differ. For simple replications my [dotfile skeleton](https://github.com/matu3ba/dotfiles_skeleton) using fd with ignorefiles worked fine for me.
I trust a manager like dotbot. With a simple command I create all the symbolic links and leave everything installed and configured. Over time I have been creating a folder structure to have all the files organized. Also, I try to browse other repositories that I find in case I see something interesting.
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