Accidentally did it again. It seems that the the file permissions are
change on every thing in all of /  (root).  Luckily I had the rooted
nautilus open, and so I was able to switch the /usr/bin and create a
working environment. I opened up gnome-panel, thus all the new programs
I lauch are in root.  Of course only programs that are running as root
will work. GDM won't work mostly likely because it does start as root.
BTW I can't access my web server because apache says "Forbidden You
don't have permission to access / on this server." I guess I put some
logs up, and see if that helps.

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file system drops dead when copying files between a rooted nautilus window and 
desktop
https://bugs.launchpad.net/bugs/245081
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