generateProjects.bat unable to work with relative path

I tried passing absolute path and relative path to generateProjects.bat, the absolute path work find, but the relative path (e.g. "..torque3d") unable to generate correct VC2005 projects (i.e. files are missing from the projects). Are there any way to make generateProjects.bat generate VC2005 projects with relative path to source files? Is the only way is to modify the generateProjects PHPs, is it going to be a lot of work?

We are using SVN and CruiseControl in our development, and we need to modify the Torque3D engine source code plus the generated VC2005 projects settings in order to integrate our existing libraries into Torque3D, thus I thought the easiest way is to include the modified generated VC2005 projects into SVN, but this won't work if VC2005 projects use absolute path to refer to the source codes.....

All suggestions on how to put Torque3D on SVN and CruiseControl are welcomed. Thanks.