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Per https://docs.python.org/3/library/sys_path_init.html, the first directory in sys.path is the current directory (when started with -m, otherwise the directory of the current script). It would seem safe to remove it, e.g. by putting del sys.path[0] in __main__.
I tried and it doesn't seem to cause any problems. Does anybody, in particular @ales-erjavec, see any problem?
I think the only thing that should be done is use the python -P | PYTHONSAFEPATH=1 python in all of the application startup scripts/shortcuts like in biolab/orange3-installers#52
Similar issue to jupyter/notebook#4892
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