I think gnome-shell could do better at ignoring programs being debugged.
It appears you can detect this by looking at the process state like in
/proc/PID/status. It will show:

State:  t (tracing stop)

Or easier to parse: Look at /proc/PID/stat and the third field will be a
lowercase 't'.

This means the process is being debugged and gnome-shell should not be
raising warnings about it.

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https://bugs.launchpad.net/bugs/1832426

Title:
  "Program" is not responding when debugging in gdb

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