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ok I checked it on several different server installation with Plesk Onyx Version 17.8.11 and it seem you are right the file manager shows the mentioned folders under the Home directory
I have to worry? can I delete the system directories like etc, var, usr, since they are not in right place? or should I leave them? can it be an error due to the fact that I restored from a dropbox backup?
Please take a look at this my video to discover the files--> screencast-2019.03.02-10-20-17
I've reinstalled my vps with ubuntu, centos, debian (always with plesk onyx): same issue!
it seems appears after I launch a simply prestashop script to update products index (maybe?)
Let me know if others plesk users have same problem.
I'm facing the same situation with my newly installer Ubuntu Server 18.04 and Plesk Onyx 17.8.11 after restoring one of my websites from backup made by Backup Manager.
We're using Ubuntu 18.04.2 and Plesk 17.8.11. FWIW The GUI Plesk Panel File Manager view of all Domains (some of which are setup quite differently than others in terms of folders and levels of folders etc) is completely normal. None of the folders mentioned in the above posts are shown, but we haven't restored any domains from backup and we don't use Prestashop.