refactor: Organized modules like they are in NixOS/nixpkgs.

flake.nix

@@ -2,6 +2,6 @@
   description = "A very basic flake";
 
   outputs = { self }: {
-    nixosModules.vagrant = { ... }: { imports = [ ./nixosModules/vagrant.nix ]; };
+    nixosModules.vagrant = { ... }: { imports = [ ./nixos/modules/virtualisation/vagrant.nix ]; };
   };
 }