I did. Fortunately, SE didn't barf when I saved the file. A restart and all the include folders were there in the project options.
But if the project doesn't have any include files yet, the Include Files tag isn't there so it's not obvious where to stick the tag. Yes I can look at the source project but even then (for a non-XML person like me) it's still hard to see where to put it.
I just think it would be easier if it was set up so that you have a block of text with one include per line. That way I can grab the block, put it in an editor window, and bulk-change all the directories as needed. (Drop your project one directories level down and see how hard it is to change the directories).