The directories of the ssh users are based on the directory of the website.
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This comes because all websites are located in /var/www (which is symlinking to /home/www ). Sure I changed all paths in Server Config accordingly.
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This can not work with a symlink as the real path is not the same then the website path. Remove the symlink and mount the directory with mount --bind instaed.
http://backdrift.org/how-to-use-bind-mounts-in-linux