I have gotten rid of the .desktop files in ~/.local/share/applications and ~/.local/share/applications/menu-xdg. I had already uninstalled menu-xdg as postings on the web had said that that would help with the duplicate icons. I never intentionally put any of these .desktop files in these directories. These files must have been put there during the normal install process. Removing these .desktop files removed all of the cruft from the other menu. I still think there is some kind of a problem here as a normal user would not know to look for the .desktop files to get rid of them. A clean install probably wouldn't have the cruft.
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