If you're File Tree pan is not showing for some reason or perhaps because you tried to make you "FILE SYSTEM" folder a "FAVORITE" then this is how to fix it.
(I left this here in case someone else runs into this issue, or Cloud9IDE can reduplicate this issue and create a preventive solution from another use encountering this.)
I found that when I refresh the page the File Tree will appear again, for a brief moment but then disappear again. The brief moment this appears is just enough time to right click on the "!fsroot" folder and it's "~" folder to click "Remove from Favorites", which will remove those folders from the Favorites list. After doing that the File Tree may still disappear, but after refreshing, things should be back to normal.