I've been through the whole Main Module thread, and I didn't see this problem addressed, so here it is:
My call-stacks, as displayed on the run tab, used to be hyperlinks to the code in which the exception was thrown. some of my code has lost its hyperlinkness. i've tried making that code be content with and without making it also a sub-source directory. i suspect that i'm doing something wrong in the Main Module configuration, but can't figure out what. Of course, it could be something else entirely (i've tried making sure that "generate debugging info" in the compile tab is set, for instance, and rebuilding everything, but that didn't fix it).