I created a subdomain and a user with FTP access
but after logging in with that user it seams on the FTP the user can navigate up the dir structure to the actual domain
How can I stop this?
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It depends on the software and how its configured. But, you can try this: in Webmin CP, go to Webmin > Servers > ProFTPd > Files & Directories. Under "Limit users to directories", select "home directory". Apply the changes.