I noticed my hosting company just changed my /home1/username/ directory to /home2/username.
I had to go through a bunch of config files and change the path. But, when I wanted to use softaculous to clone one of my sites I kept getting this error.
You cannot clone the installation in a subdirectory of the original installation
Well, after a while I noticed that path of the original installation in the info section (which isn't changeable, at least in that panel) said /home1/ I have different domains and use the /home2/unername/backup to store the data. Both are outside that domain. But it still throws up that error. It must be because of the path of the original in sofaculous is set to the home1.