setup Grails project with in-place plugins

I have the following directory structure

--myApp
   |
   |--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 fuse-view/fuse-view-web

  
  

  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 is a duplicate. My guess is that this is because IntelliJ  is also finding these classes in

main-app/plugins

.
Is there a way to prevent this, or some other way of correctly  setting up a Grails app and some in-place plugins as a single IntelliJ  project. I'm using Grails 1.3.7 and IntelliJ 10.5.4