OK, found out what was causing all the troubles (at least I think
so): For the subprojects to work properly, they need to share the
"build" folder with the main TeXShop.xcodeproj.
To do that, I set their build path dirs to be "../../build". My
mistake: I set them on the "General" pane of the Project settings
(i.e. the "Place Build Products In:" setting). Turns out that those
settings are user specific, and hence were never commited to the
Simple fix: I removed the setting there, then went to the "Build" tab
of the same dialog, and update the "Build Products Path" setting for
all configurations to be "../../build".
Now it works fine, at least over here, in all my checkouts.
Hopefully, it fixed the troubles you were having, too. Sorry for all
the mess :-/.