Update to (somewhat?) dendritic pattern

Heavily inspired by https://github.com/Doc-Steve/dendritic-design-with-flake-parts.

> Atomic commits? Never heard of them!

modules/nix/tools/home-manager.nix

@@ -0,0 +1,23 @@
+{ inputs
+, config
+, ...
+}: {
+  # Add home-manager input
+  flake-file.inputs = {
+    home-manager.url = "github:nix-community/home-manager/release-25.11";
+    home-manager.inputs.nixpkgs.follows = "nixpkgs";
+  };
+
+  imports = [ inputs.home-manager.flakeModules.home-manager ];
+
+  flake.modules.nixos.home-manager = {
+    imports = [
+      inputs.home-manager.nixosModules.home-manager
+    ];
+
+    home-manager = {
+      verbose = true;
+      useGlobalPkgs = true;
+    };
+  };
+}

modules/nix/tools/secrets.nix

@@ -0,0 +1,26 @@
+{ inputs, ... }: {
+  flake-file.inputs = {
+    agenix = {
+      url = "github:ryantm/agenix";
+      inputs.nixpkgs.follows = "nixpkgs";
+      inputs.home-manager.follows = "home-manager";
+    };
+    secrets = {
+      url = "path:./secrets";
+      flake = false;
+    };
+  };
+
+  flake.modules.nixos.secrets = { pkgs, ... }: {
+    imports = [
+      inputs.agenix.nixosModules.default
+    ];
+    environment.systemPackages = [ inputs.agenix.packages.${pkgs.stdenv.hostPlatform.system}.default ];
+  };
+
+  flake.modules.homeManager.secrets = { pkgs, ... }: {
+    imports = [
+      inputs.agenix.homeManagerModules.default
+    ];
+  };
+}