Anyone else upgrade to El Capitan only to have all their folders disappear? Looks like all my files are still there but they are all under "All my files", years worth of archiving gone! Any help would be much appreciated :)
'All My Files" is just a Smart folder (& frankly, imho, a useless one ;-)
Your files should be right where you left them in the hierarchy - right click one & 'Show in Enclosing Folder' to see where it really is.
The default behaviour is that new Finder windows show "All My Files" But you can easily change this to open anywhere you like.
Go to Finder, press Cmd ⌘ , (or Finder menu > Preferences… )
Select General & then choose your preferred initial location from the drop menu