It's a bit of a mess at the moment for historical reasons. The shipped files are from what we call the "Mission" edition, which is basically the complete repository. This has the Source directory/folder. Gerald is busy redoing all the scripts for our CI server cluster.
Until he has finished this, you'll have to hand edit the scripts. The ones that you really need are called RebuildXXX.bat/sh. They do the main cross-compile and second/third stage rebuilds.
Since most people only run one O/S we are not concentrating on the Mission scripts except for internal build use. My suggestion for the moment would be to make one file that configures directory macros for your configuration. If you do this, we will happily discuss your solution for incorporation.