refactor(flake): extract more stuff in flake modules

`pkgs` redefinition (with overlays)
`nix-topology` setup
`agenix-rekey` setup

nix/agenix.nix

@@ -0,0 +1,15 @@
+{ lib, config, self, inputs, ... }:
+
+{
+  imports = [
+    inputs.agenix-rekey.flakeModule
+  ];
+
+  perSystem = {
+    agenix-rekey = {
+      nodes = {
+        inherit (self.nixosConfigurations) jeeves;
+      };
+    };
+  };
+}

nix/pkgs.nix

@@ -0,0 +1,13 @@
+{ lib, config, self, inputs, ... }:
+
+{
+  perSystem = { lib, pkgs, system, ... }: {
+    _module.args.pkgs = import inputs.nixpkgs {
+      inherit system;
+      overlays = lib.attrValues self.overlays ++ [
+        inputs.nix-topology.overlays.default
+      ];
+      config = { };
+    };
+  };
+}

nix/topology.nix

@@ -0,0 +1,23 @@
+{ lib, config, self, inputs, ... }:
+
+let
+  modules = [
+    {
+    }
+  ];
+in
+{
+  imports = [
+    inputs.nix-topology.flakeModule
+  ];
+
+  perSystem = {
+    topology = {
+      inherit modules;
+      nixosConfigurations = {
+        inherit (self.nixosConfigurations)
+          jeeves;
+      };
+    };
+  };
+}