Remove pirate usage of Nix

Apparently Nix 2.24 doesn't like dirty git repos
("lock file contains unlocked input") and makes it known by failing,
which tipped me that I wasn't using Lix everywhere.

flake.nix

@@ -78,9 +78,15 @@
         };
         flakeTools = { self }: flake-utils.lib.eachDefaultSystem (system:
           let
-            pkgs = import nixpkgs (nixpkgsConfig // {
-              inherit system;
-            });
+            pkgs = import nixpkgs
+              (nixpkgsConfig // {
+                inherit system;
+                # We do an overlay here so nixos-rebuild and other use lix.
+                # We don't do an overlay for the whole system because lix is not binary compatible.
+                overlays = [
+                  (self: super: { nix = super.lix; })
+                ];
+              });
           in
           {
             apps = {