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An alternative is to write a Nix wrapper for Emacs with the dependencies in PATH: https://github.com/akirak/emacs.d/blob/maint/flake.nix. Then I use nix run to start Emacs. I don't think this is recommended in this community, but it works for me.
Instead of defining extra Emacs packages in Nix, you can use emacsWithPackagesFromUsePackage function from emacs-overlay.
I'm not that adept with nix either, unfortunately, so I can't decipher that much from either the home-manager source or the nixpkgs source. It does add a default.el and some site-start stuff, but I'm not sure why that would mess with your init file.
I'm not that adept with nix either, unfortunately, so I can't decipher that much from either the home-manager source or the nixpkgs source. It does add a default.el and some site-start stuff, but I'm not sure why that would mess with your init file.