When there's a new release of WSN Knowledge Base, your admin panel notifies you and prompts you to click to upgrade. If you click this button, it'll download and apply the latest release and leave you with instructions for any template changes which may be needed. In order for it to have the permissions to do this, you must either have supplied FTP info or be running PHP as CGI (rather than as an apache module).

When PHP is run as an apache module, using the automatic upgrade will result in all the PHP files being owned by apache's user rather than your FTP user. As a result, attempting to overwrite files via FTP will henceforth fail. To work around this, if you want to overwrite via FTP you need to delete the files first. If you're seeking to overwrite everything to do a non-automatic manual upgrade, you'll want to delete everything except these items: config.php, /templates/, /languages/, /integration/, /attachments/, /plugins/, /cache/, /javascript/. Another option would be to use the CHMOD utility to make everything 777, but that's considered poor security practice.