setup Grails project with in-place plugins

I have the following directory structure

--my-app
   |
   |--main-app
   |
   |--plugins
      |
      |--plugin1
      |
      |--plugin2

In grails-app/conf/BuildConfig I've added the necessary configuration to ensure that the plugins are loaded from the

plugins

directory, so that when I run the application, it picks up the most recent changes. I'm trying to set this up as a single project in IntelliJ which has 3  modules, one for the main application and one for each of the two  plugins. I tried the following:

• Generate the IntelliJ project files

     cd my-app/main-app

     grails integrate-with --intellij

• Open the generated .ipr file from inside Intellij (File | Open  Project...). This adds the main application and plugins as Grails  modules

However every time I open a class from a plugin, IntelliJ reports  that the class has two occurrences. It seems each plugin class is being  detected

1. once in the IntelliJ module for the plugin itself
2. once in the module that IntelliJ automatically creates which contains all the plugins. In my case, this module is named

   main-app-grailsPlugins

In the project structure view I tried removing the content roots for

plugin1

and

plugins2

from main-app-grailsPlugins, but they get automatically added back again.
Is there a way to prevent this, or some other way of correctly  setting up an IntelliJ project for a Grails app with in-place plugins.  I'm using Grails 1.3.7 and IntelliJ 10.5.4