Package your user's emacs init.el etc. in to your nix emacs itself

emacs-init-as-a-package.nix

{ pkgs ? import <nixpkgs> {} }:
let
  emacsPackaging = pkgs.emacsPackagesNg;

  my-mode = emacsPackaging.trivialBuild {
    pname = "my-mode";
    version = "1970-01-01";
    src = pkgs.writeText "default.el" ''
      (global-set-key (kbd "<end>") 'end-of-line)
      (global-set-key (kbd "<home>") 'beginning-of-line)


      (defun loader-after-plugins ()
            (define-globalized-minor-mode global-fci-mode fci-mode (lambda () (fci-mode 1)))
      	    (global-fci-mode 1)
            (editorconfig-mode 1)

            (require 'notmuch)
            (global-set-key (kbd "C-c m") `notmuch)
      )
      (add-hook 'after-init-hook #'global-flycheck-mode)
      (add-hook 'after-init-hook #'loader-after-plugins)

    '';
  };
in
(emacsPackaging.emacsWithPackages (epkgs: with epkgs.melpaPackages; [
  nix-mode
] ++ [
  pkgs.notmuch
  my-mode
]))