diff --git a/flight/commands/ControllerCommand.php b/flight/commands/ControllerCommand.php
index 9706d97..cfea2ae 100644
--- a/flight/commands/ControllerCommand.php
+++ b/flight/commands/ControllerCommand.php
@@ -29,7 +29,7 @@ public function __construct(array $config)
     public function execute(string $controller)
     {
         $io = $this->app()->io();
-        if (isset($this->config['app_root']) === false) {
+        if (isset($this->config['runway']['app_root']) === false) {
             $io->error('app_root not set in .runway-config.json', true);
             return;
         }
@@ -38,7 +38,7 @@ public function execute(string $controller)
             $controller .= 'Controller';
         }
 
-        $controllerPath = getcwd() . DIRECTORY_SEPARATOR . $this->config['app_root'] . 'controllers' . DIRECTORY_SEPARATOR . $controller . '.php';
+        $controllerPath = getcwd() . DIRECTORY_SEPARATOR . $this->config['runway']['app_root'] . 'controllers' . DIRECTORY_SEPARATOR . $controller . '.php';
         if (file_exists($controllerPath) === true) {
             $io->error($controller . ' already exists.', true);
             return;
@@ -86,6 +86,6 @@ public function execute(string $controller)
     protected function persistClass(string $controllerName, PhpFile $file)
     {
         $printer = new \Nette\PhpGenerator\PsrPrinter();
-        file_put_contents(getcwd() . DIRECTORY_SEPARATOR . $this->config['app_root'] . 'controllers' . DIRECTORY_SEPARATOR . $controllerName . '.php', $printer->printFile($file));
+        file_put_contents(getcwd() . DIRECTORY_SEPARATOR . $this->config['runway']['app_root'] . 'controllers' . DIRECTORY_SEPARATOR . $controllerName . '.php', $printer->printFile($file));
     }
 }
diff --git a/flight/commands/RouteCommand.php b/flight/commands/RouteCommand.php
index bbcf52e..1b2691d 100644
--- a/flight/commands/RouteCommand.php
+++ b/flight/commands/RouteCommand.php
@@ -41,7 +41,8 @@ public function execute()
     {
         $io = $this->app()->io();
 
-        if (isset($this->config['index_root']) === false) {
+        
+        if (isset($this->config['runway']['index_root']) === false) {
             $io->error('index_root not set in .runway-config.json', true);
             return;
         }
@@ -50,7 +51,7 @@ public function execute()
 
         $cwd = getcwd();
 
-        $index_root = $cwd . '/' . $this->config['index_root'];
+        $index_root = $cwd . '/' . $this->config['runway']['index_root'];
 
         // This makes it so the framework doesn't actually execute
         Flight::map('start', function () {
diff --git a/tests/commands/ControllerCommandTest.php b/tests/commands/ControllerCommandTest.php
index 510aaa2..f4903a2 100644
--- a/tests/commands/ControllerCommandTest.php
+++ b/tests/commands/ControllerCommandTest.php
@@ -67,7 +67,7 @@ public function testControllerAlreadyExists(): void
         $app = $this->newApp('test', '0.0.1');
         mkdir(__DIR__ . '/controllers/');
         file_put_contents(__DIR__ . '/controllers/TestController.php', '<?php class TestController {}');
-        $app->add(new ControllerCommand(['app_root' => 'tests/commands/']));
+        $app->add(new ControllerCommand(['runway' => ['app_root' => 'tests/commands/']]));
         $app->handle(['runway', 'make:controller', 'Test']);
 
         $this->assertStringContainsString('TestController already exists.', file_get_contents(static::$ou));
@@ -76,7 +76,7 @@ public function testControllerAlreadyExists(): void
     public function testCreateController(): void
     {
         $app = $this->newApp('test', '0.0.1');
-        $app->add(new ControllerCommand(['app_root' => 'tests/commands/']));
+        $app->add(new ControllerCommand(['runway' => ['app_root' => 'tests/commands/']]));
         $app->handle(['runway', 'make:controller', 'Test']);
 
         $this->assertFileExists(__DIR__ . '/controllers/TestController.php');
diff --git a/tests/commands/RouteCommandTest.php b/tests/commands/RouteCommandTest.php
index 0d2aee7..993599c 100644
--- a/tests/commands/RouteCommandTest.php
+++ b/tests/commands/RouteCommandTest.php
@@ -101,7 +101,7 @@ public function testGetRoutes(): void
     {
         $app = @$this->newApp('test', '0.0.1');
         $this->createIndexFile();
-        $app->add(new RouteCommand(['index_root' => 'tests/commands/index.php']));
+        $app->add(new RouteCommand(['runway' => ['index_root' => 'tests/commands/index.php']]));
         @$app->handle(['runway', 'routes']);
 
         $this->assertStringContainsString('Routes', file_get_contents(static::$ou));
@@ -127,7 +127,7 @@ public function testGetPostRoute(): void
     {
         $app = @$this->newApp('test', '0.0.1');
         $this->createIndexFile();
-        $app->add(new RouteCommand(['index_root' => 'tests/commands/index.php']));
+        $app->add(new RouteCommand(['runway' => ['index_root' => 'tests/commands/index.php']]));
         @$app->handle(['runway', 'routes', '--post']);
 
         $this->assertStringContainsString('Routes', file_get_contents(static::$ou));