Re-organize Nix Modules

- Move all programs into system folder
- Create `default.nix` for each folder to reduce number of imports
  in configuration.nix
- Rename some modules to be more generic and less package
  specific to allow for easy swapping of programs in the future
- Update flake.lock

system/programs/utilities/default.nix

@@ -0,0 +1,11 @@
+{ config, lib, pkgs, ... }:
+
+{
+  imports = [
+    ./3d-printing.nix
+    ./bootable-media.nix
+    ./file-syncing.nix
+    ./keyboard-configuration.nix
+    ./passwords.nix
+  ];
+}