Many thanks for the explanation of the problem, and in advance for this potential enhancement.
The reason that I want to split things out is that the projects that my employers work on tend to have several subfolders for sources, e.g.
longpath/project/
longpath/project/sources
longpath/project/sources/includes
longpath/project/sources/appstuff
longpath/project/sources/libstuff
longpath/project/derivedincludes
longpath/project/logs
longpath/project/data
longpath/project/output
This makes it easier to dump off the sources to backup media as an entire tree but omit any derived or intermediate files, e.g. *.OBJ, and data & log files, and then add the few other vital files to the project root, e.g. *.BAT, *.PPJ and *.PPX. Because I have become used to this fairly simple but effective tactic, I tend to use it for my own projects when they become a bit too complex to keep track of in a single folder.