1. how to clean my site properly?
Never had to deal with it, so I don't know. Normally, I would backup the database, delete everything, and reinstall from scratch, and then restore the database.
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2. How to install protector as I can not install it. I followed the instructions but dont seem to see the module when i log onto the site. All of my files are in the /htdocs/ and I dont have a XOOPS trust path. I though if using an empty folder i ve called private? is this possible.
Turn on the "Debug" and see the error messages.
You probably don't have anything in the trustpath, which should be defined in the mainfile.php, or you didn't define the trustpath in the first place. So start there...