- /.ssh -> Stores rsa keys
- /logs -> Stores the Error logs and the Access logs for your site
- /webroot -> The root directory for your website.
Within the /webroot folder the permissions on your files should be 755 (or 644 for non executable files, e.g. pictures) with the user and group as your sites name. The webroot folder itself should not be altered as it is secured so that other sites on the server are disabled access. At no point should you assign the everyone group write permission to any file! (e.g. xx7, xx6, xx3, xx2)
For more information please see: http://en.wikipedia.org/wiki/Filesystem_permissions
(example used for hosting.susu.org)