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.
It looked like this... @Screenshot
I started picking frequently used folders as "Favorites", by right clicking the folder in the file tree and adding it as a "Favorite". @Screenshot
After doing so I decided I would rather have the Root directory folders above the Favorite folders, but collapsed. This way if I need to get to a new folder (one that isn't a favorite) I can do so quickly without having to scroll through my list of favorites just to get to the root path folders.
So I dragged the top Title Text "FILE SYSTEM" area above the root path folders and tried to drop it above the "FAVORITES" section. It didn't quite go above that area but would right below, so I dropped it there to see if this would work for me.
After it finished reloading the new dropped folder it came out like this... @Screenshot
When I clicked the dropdown arrow for "!fsroot" subfolder content would show.
So I then I tried to drag and drop this folder back out of the favorites and that is when the File Tree disappeared.
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.