diff --git a/flake-module.nix b/flake-module.nix
index f101833..958d27f 100644
--- a/flake-module.nix
+++ b/flake-module.nix
@@ -279,7 +279,7 @@ let
 
   configurationOptions = configType: {
     modulesDirectory = mkOption {
-      default = "${cfg.root}/${configType}-modules";
+      default = if cfg.root != null then "${cfg.root}/${configType}-modules" else ./unset-directory;
       defaultText = literalExpression "\"\${ezConfigs.root}/${configType}-modules\"";
       type = types.pathInStore;
       description = ''
@@ -288,7 +288,7 @@ let
     };
 
     configurationsDirectory = mkOption {
-      default = "${cfg.root}/${configType}-configurations";
+      default = if cfg.root != null then "${cfg.root}/${configType}-configurations" else ./unset-directory;
       defaultText = literalExpression "\"\${ezConfigs.root}/${configType}-configurations\"";
       type = types.pathInStore;
       description = ''
@@ -375,7 +375,8 @@ in
 {
   options.ezConfigs = {
     root = mkOption {
-      type = types.pathInStore;
+      default = null;
+      type = types.nullOr types.pathInStore;
       example = literalExpression "./.";
       description = ''
         The root from which configurations and modules should be searched.
@@ -398,7 +399,7 @@ in
     darwin = configurationOptions "darwin";
   };
 
-  config.flake = mkIf (cfg ? root) rec {
+  config.flake = rec {
     homeModules = readModules cfg.home.modulesDirectory;
     nixosModules = readModules cfg.nixos.modulesDirectory;
     darwinModules = readModules cfg.darwin.modulesDirectory;
diff --git a/template/darwin-configurations/.gitkeep b/template/darwin-configurations/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/template/darwin-configurations/dummy b/template/darwin-configurations/dummy
deleted file mode 100644
index 9c558e3..0000000
--- a/template/darwin-configurations/dummy
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/template/darwin-modules/.gitkeep b/template/darwin-modules/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/template/darwin-modules/dummy b/template/darwin-modules/dummy
deleted file mode 100644
index 9c558e3..0000000
--- a/template/darwin-modules/dummy
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/template/flake.nix b/template/flake.nix
index 939b88f..22a2aa3 100644
--- a/template/flake.nix
+++ b/template/flake.nix
@@ -42,9 +42,6 @@
       systems = [ ];
 
       ezConfigs = {
-        # All subdirectories under this contain a `dummy` file.
-        # They can be deleted after the template has been initialised.
-        # They are only there to preserve the directory structure within git.
         root = ./.;
         globalArgs = { inherit inputs; };
       };
diff --git a/template/home-configurations/.gitkeep b/template/home-configurations/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/template/home-configurations/dummy b/template/home-configurations/dummy
deleted file mode 100644
index 9c558e3..0000000
--- a/template/home-configurations/dummy
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/template/home-modules/.gitkeep b/template/home-modules/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/template/home-modules/dummy b/template/home-modules/dummy
deleted file mode 100644
index 9c558e3..0000000
--- a/template/home-modules/dummy
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/template/nixos-configurations/.gitkeep b/template/nixos-configurations/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/template/nixos-configurations/dummy b/template/nixos-configurations/dummy
deleted file mode 100644
index 9c558e3..0000000
--- a/template/nixos-configurations/dummy
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/template/nixos-modules/.gitkeep b/template/nixos-modules/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/template/nixos-modules/dummy b/template/nixos-modules/dummy
deleted file mode 100644
index 9c558e3..0000000
--- a/template/nixos-modules/dummy
+++ /dev/null
@@ -1 +0,0 @@
-.
diff --git a/unset-directory/.gitkeep b/unset-directory/.gitkeep
new file mode 100644
index 0000000..e69de29