Ahh, finally I have discovered a workaround.  This command, executed in
a TTY (which I can access with ctrl-alt-F5 or similar), seems to gently
restart gnome-shell and give me everything back with my applications all
still running:

dbus-send --type=method_call --print-reply --dest=org.gnome.Shell
/org/gnome/Shell org.gnome.Shell.Eval string:'global.reexec_self()'

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https://bugs.launchpad.net/bugs/1181666

Title:
  gnome-shell randomly blocks mouse clicks from working in app windows

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