@Override
protected void injectDesktopExtensions(List<IDesktopExtension> desktopExtensions) {
  DesktopExtension extension = new DesktopExtension();
  extension.setCoreDesktop(this);
  desktopExtensions.add(extension);
}

1. create core application
   [Scout View] Create a new Scout project with name org.example.myapp and postfix core. This will create bundles with names org.example.myapp.[client|shared|server].core
   
2. create extension bundles
   [Java View] Manually create three bundles (plug-in projects) with names org.example.myapp.[client|shared|server].extension. The naming pattern is important (the postfix extension should reflect the name of your module, though).
   
3. set-up bundle dependencies
   [Java View] Open the manifest editor for all three bundles and define bundle dependencies:
   
   org.example.myapp.client.extension depends on org.eclipse.scout.rt.client and org.example.myapp.shared.extension.
   
   org.example.myapp.shared.extension depends on org.eclipse.scout.rt.shared. Re-export this dependency!
   
   org.example.myapp.server.extension depends on org.eclipse.scout.rt.server and org.example.myapp.shared.extension.
   
4. make your bundles Scout bundles
   [Scout View] Use menu "Import Plugin..." on the "Scout Projects" folder and import all three extension bundles. Restart Eclipse.
   
5. create a desktop extension
   [Java View] Create a new class in the
   org.example.myapp.client.extension bundle: org.example.myapp.client.extension.ui.desktop.DesktopExtension which inherits from org.eclipse.scout.rt.client.ui.desktop.AbstractDesktopExtension
   
6. building the extension
   [Scout View] The Scout SDK now displays your three extension bundles as a separate Scout module. The orange client node also contains a "Desktop-Extension" node. You can now use the Scout SDK to build your module as you would with a normal Scout application. Well, almost. There are a few further caveats: You also need to create a separate TextProviderService for your extension module (do this in the corresponding folder in the shared bundle).
   Also, when adding a new outline to the desktop extension, the generated Java code did not compile in my test. You need to fix this manually: In the constructor of the generated OutlineViewButton change Desktop.this to getCoreDesktop() and you should be fine.
   You might stumble over some more issues like this, but all of them can be resolved in one way or another :)
   
7. integrate with the core application
   Finally we're back to your initial question :) We now have a desktop extension class which we will integrate to the core application.
   
   [Java View] Open the manifest editor for the client extension bundle. Export the package containing the desktop extension class (org.example.myapp.client.extension.ui.desktop).
   Open the manifest editor for the client core bundle. Import the above package from the client extension bundle.
   
   Adapt the product files for both the client and server products. Add the extension bundles to the dependencies (client and shared bundles in the client product, server and shared in the server product).
   
   In the Desktop class of the client core bundle, override the method injectDesktopExtensions() and add an instance of the desktop extension class to the list of extensions (see above).
   

I could maybe be wrong, but in my opinion, modules bundles should be bases bundles' fragments (rather than plugins).
It would thus help avoid cycles when importing classes as it appears here:

@Override
protected void injectDesktopExtensions(List<IDesktopExtension> desktopExtensions) {
	DesktopExtension extension = new DesktopExtension();
	extension.setCoreDesktop(this);
	desktopExtensions.add(extension);
}

furthermore make developed modules optional!

Where it's still time, the development team should take this into account dor SDK production ... if I'm somewhat right