xCloner have brought out an update for this.
They don't provide details on how to upgrade the standalone script, so I am detailing what I did on my copy that I use with Zen Cart...
1. Back up everything of course
2. Delete the old xcloner folder on your server
3. Upload the new script with the same folder name
4. Replace the new /cloner.config.php file with your old one
5. Add any extra files from your /configs folder to the new one.
More detailed version:
1. First thing is to back up your site before making any changes - Oh wait, XCloner does that automatically already :)
2. Just in case, I made a quick compressed copy of the xcloner folder with "File Manger" through cPanel in my web host's interface. Leave the compressed copy on the server till you are happy it is all working.
3. I made downloaded the following files / folders:
The configs folder contains any custom cron commands/pages you made. e.g. I run 2 commands:
(a) A simple database back-up every night
(b) A full file site files back up once a week.
The cloner.config.php is all your configuration for your site, making xcloner specific to you including your xcloner user name and password.
4. I deleted all the contents of the xcloner folder on my server
5. I uploaded all the contents of the new upgrade to the server into the xcloner folder.
(I did it this way rather than just uploading the new upgrade and over writing, as there were some differences in the file structure.)
6. After the new files were uploaded, I copied my old /configs files and the cloner.config.php file overwriting the new ones. This way I kept all my settings.
7. I went in and ran the cron jobs, just to see it was all working fine, which it appears to be.
8. I deleted the compressed 'old xcloner folder' off the server. I still have a local copy though, just in case. I am big into backups - too many catastrophes from not backing up.
Anybody who does any work on their own Zen Cart will have no problems with this process, it simple.
I hope this works for you.