Is that even possible? I'd have to tell gdb to exit from the
XQueryPointer function in the main thread any time it stops the program
- whether I just attached it, or hit Ctrl-C, or the program hit a
breakpoint in some other thread. I've no idea how to do that.

I've debugged the same program in Windows and OS X - and neither OS has
this problem.

Also, the documentation for XQueryPointer does not say that it can block
forever. So I think it's a bug.

-- 
X server freezes while the application is executing XQueryPointer
https://bugs.launchpad.net/bugs/400374
You received this bug notification because you are a member of Ubuntu-X,
which is subscribed to xorg-server in ubuntu.

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