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I can't reproduce but it happened to me during testing MDL-42020. On master only.
PHP Warning: mkdir(): File exists in /home/jerome/moodles/integration_master/moodle/lib/setuplib.php on line 1258, referer: http://jerome.moodle.local/m/integration_master/course/index.php?categoryid=2
So it's just more of an alert if you can detect anything wrong there. Otherwise close it.
PHP Warning: mkdir() logged during upgrade and upon purge cache
Performance improvement in course listings