We have a web portal product from which we customize portals from customers. We use the precompiled web app and create a virtual directory (vd) where the customization resides. In addition to this we do some changes web.config in the web app folder. We would obviously like to keep these customizations under TFS source control.

When I try to add the precompiled web app (which I don't want to add to source control), a warning tells me that the vds cannot be added. If I only add the folder that is referenced to by the vd, I lose the references to assemblies in the precompiled web app.

My questions are:

1. How do I structure a solution for adding IIS (sub application level) virtual directories and still retain the references to assemblies?
2. Is it possible to add other directories/files from the web application level (like App_Theme, web.config etc.) to the solution?

Since we already use Visual Source Safe, we have established a tree structure for each customization project:

Project Root
|
|-Custom Sql
|
|-Custom Portal Files (which is added as a virtual directory)
|
|-Other Customizations

I could probably do a lot of this manually through the source control explorer, but I'd like to have everything done through a solution.

I've followed the instructions using this article: http://msdn.microsoft.com/en-us/library/bb668986.aspx, but this doesn't address the exact problem that I have. Oh, and we are currently using Visual Source Safe for portal customizaton, but are eager to make the move to TFS.

TIA