I am starting to use Wolfram Workbench 2.0 to consolidate a project and take advantage of subversion to keep track of my ongoing updates and changes. The project is compartmentalized into 5 individual Mathematica Application projects, one of which I have set up to have the property that it references the other 4. The compartmentalization is very handy for organization and deploying Project A so that it includes the others makes sharing the application very easy, with one exception.
I have found that the only obvious consequence of setting the property of Project A to reference Projects B, C .. etc is that when you Deploy the application of Project A to an archive, the referenced projects are included in the .zip. Everything, that is, except for the Documentation for each referenced project.
I have documentation built for every project, and each individual project deploys with Documentation just fine. I can't think of why the Documentation would be excluded for each Referenced project, is this intended behavior?