I appear to have gotten around the root problem at GoDaddy.

For a couple of months I ran with DNN installed in the /dnn directory and redirect .htm pages redirecting my old 10 page web site to the matching DNN pages. However, this setup really screwed me up with the search engines and with the referrer info in the site log which I use to know how people got to the web site. I was further screwed up by GD when they managed to reset directory permissions and I realized that I would have to manually reset them at every level in the tree. It was easier to ftp the entire tree to my local system, delete the lower level directories, reset the permissions on the top level ones and ftp the files back to GoDaddy.

I then realized that it I created directories with the correct permissions in root for /Portals, /DesktopModules, /Install, /App_Code, Config & /backup I and placed the files at the top level I might be able to get rid of the /dnn in my URL and the redirection.

It works OK because DNN doesn't need write access to items in the root directory very often. The only two I have discovered is during the install install (to change the machineKey in web.config) and when manually restaring the application. If I need to manually restart the application I just 'touch' web.config and that does the trick.

I will complain to GoDaddy about a backup/restore of the database. That would also make my life easier and better