refactor: flatten the single-file lib and system directories

Each held one default.nix, so the directory added a level to descend without
grouping anything. They are now lib.nix and system.nix beside flake.nix, which
reads as the flake's own scaffolding.

The shared base config's reference to the shared secrets file was relative to
the directory it sat in, so it moves with the file.

Verified to build the same system toplevel as before the move.

flake.nix

@@ -49,7 +49,7 @@
     { self, nixpkgs, ... }@inputs:
     let
       inherit (nixpkgs) lib;
-      my = import ./lib { inherit lib inputs self; };
+      my = import ./lib.nix { inherit lib inputs self; };
     in
     {
       # Helper functions for discovering and building hosts.