Hi Rob,
There are utilities you can run from the command to create and build CCS projects. See:
http://processors.wiki.ti.com/index.php/Projects_-_Command_Line_Build/Create
Example:
> eclipsec –noSplash -data "C:\Path\To\MyWorkspace" -application com.ti.ccstudio.apps.projectBuild -ccs.projects MyProject -ccs.configuration Debug
Thanks
ki