In my opinion a webftp client like ajax explorer or net2ftp should stay a separate package like the webmail (roundcube, squirrelmail) and mysql (phpmyadmin) webclients. So each admin has the choice which FTP clients he wants to use and if he wants to use a webftp client at all.
If ajaxexplorer is a FTP client, it should be able to authenticate itself by FTP login like any other client?
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