Note, what you are trying to do here isnt an intended way for the system to be used. You cannot do a cleanup really without upgrading your site to the latest release of the platform, unless you happen to have a copy of the files. The correct way to clean things up from older installs if needed would be
Create a FULL backup
delete all files/folders apart from
uploads
conf_global.php
constants.php (if you have one)
.htaccess
Upload a fresh set of files from your client area
Note, this would not in any way account for 3rd party items. So you may have folders in the applications folder from 3rd party items you need to keep, and also the plugins folder if you have any plugins. Also note, the above is based on your being on the latest release