Seeking better answer about terminal emulation
Answered
In this stackoverflow response, I gave an incorrect reason, but proper solution to the askers problem. Since it was selected as the correct answer, I would like to update the reasoning. Thanks
https://stackoverflow.com/questions/65031238/why-doesnt-os-systemcls-clear-the-recent-output/65032564#65032564
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Our Run window doesn't support some of the things that one can do in the terminal. One of them is clearing the output.
When trying to clear the output in a 'non-terminal' output window, PyCharm even shows that the TERM environment variable is not set.
Setting that variable manually may help in some cases, but other terminal-specific things are still missing, which is why we have an option to emulate the terminal in the Run window.