I installed CCNET to make autobuild from a GIT server. I have a big problem here : My Git Server Repo Structure :
Repo.git
--- Module 1(Folder 1)
In Git, if you have several directories that are always checked out independently, then these are really two different projects and should live in two different repositories. You can merge them back together at a later point using Git Submodules
An alternative approach you can use Modification Writer Task. This tasks writes to an XML file, which can be evaluated from build script or batch file. Based on this you can do your build.