Do not call isolate_namespace on the application

What we want to test is that two different calls to isolate_namespace
with the same module doesn't change the original railtie. We can do that
defining two different railties.

We can't call in the application because this method is not supposed to
be called in an Application class.

railties/test/railties/engine_test.rb

@@ -882,7 +882,15 @@ YAML
         end
       RUBY
 
-      add_to_config "isolate_namespace AppTemplate"
+      @plugin.write "lib/new_lugin.rb", <<-RUBY
+        module AppTemplate
+          module NewPlugin
+            class Engine < ::Rails::Engine
+              isolate_namespace(AppTemplate)
+            end
+          end
+        end
+      RUBY
 
       app_file "config/routes.rb", <<-RUBY
         Rails.application.routes.draw do end