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You use ~/.emacs.d/init.el and just symlink that file to ~/.emacs, just in case some other programs / plugins expect to find .emacs. On a macOS or GNU/Linux system, the command would be: ln -s ~/.emacs.d/init.el ~/.emacs This way you get all the benefits of VC of your ~/emacs.d directory structure and you'll be able to use a shorter name when you need to ...


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