refactor(flake): move flake modules into separate subdirectories

Also put `outputs` before `inputs` in `flake.nix` (readability)

modules/flake/agenix/default.nix

@@ -0,0 +1,13 @@
+{ lib, config, self, inputs, ... }:
+
+{
+  imports = [
+    inputs.agenix-rekey.flakeModule
+  ];
+
+  perSystem = {
+    agenix-rekey = {
+      nodes = self.nixosConfigurations;
+    };
+  };
+}