Following up on this: it is not quite so dire as I had originally thought, just horribly confusing (and still fundamentally broken). When you click an app icon after the GUI first comes up, it will move the main GUI to the background, and the
menus will change to the menus for the specific app, but the app window doesn't actually appear. Clicking on the dock icon for the active GUI magically brings all windows to the foreground, and after that windows seem to appear normally. So it is ultimately
usable, in theory. I will keep poking at this but I can't see anything wrong in our code, and the font-related error messages are certainly not going away easily.
PS. Apple helpfully resets the security settings when you upgrade, so attempting to install a new version of Phenix is going to pop up an error about us not being a registered developer. You can un-break it by changing the security settings to
allow apps from anywhere to be installed. I'll see if there's a solution to this that doesn't involve giving Apple 30% of our NIH grants.
-Nat