Thanks for the reply.
The output stealing focus repeatedly would only happen while the game is actively compiling, so you might only notice it if compiling a large project that takes a long time. After compile is done it was no longer a problem. I have checked with my girlfriend if she is also experiencing the same issue and she confirms that she is (we do work on the same project though).
The big issue for me though, was more that it auto focuses at all. even on small projects when you compile it will open the output window and focus it when you initially hit F5, which can be quite annoying if you don't need to see the output and want to continue working.
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Thanks for the constructor rec, I will try it out.