Do flakes also set the system channel?

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I don’t know if this is best practice, but this is what I do:

let nixPath = "/etc/nixPath";

in
{
  systemd.tmpfiles.rules = [
    "L+ ${nixPath} - - - - ${pkgs.path}"
  ];

  nix = {
    nixPath = [ "nixpkgs=${nixPath}" ];
  };
}

Instead of using /etc/nixPath, you could of course also just set the NIX_PATH environment variable, but that would require closing terminals in order to pick up the new value, so the on-disk version is more flexible.

EDIT: just to clarify, doing this means that all your regular nix-* tools work as expected with flakes.

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