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Look at my comment above. It isn’t a flake but it does install emacs-overlay. I used this for inspiration: https://github.com/doomemacs/doomemacs/blob/master/shell.nix
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Just had a quick look, looks like you are trying to use the programs.emacs module, but you are not importing the emacs overlay into your home-manager environment. So the pkgs variable would not be referring to the same thing in your system packages and your home-manager packages. That would be my guess. I don't have this issue as I simply use home-manager as a module in my system configuration instead of using it as a standalone tool. See installation instructions here https://github.com/nix-community/home-manager for more info on that.