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)
the answer from @domu904 is correct.
But if you do not want to change your project structure you can try to use the Filtered Source Control.
With the Filtered Source Control you're abel to specify include and exclude filter rules for CCNet to detect modifications.
So you can include just the specific git module folder in your module ccnet project.
To trigger the dependend module ccnet projects use the Project Trigger.