Maybe if they just include a hook to the Eclipse shell, as an (optional) layer above the fs, they can get the versioning/collaboration "for free". IMHO, that's the only very interesting part of this problem. The rest is just the classic (yet still never quite settled) question of how best to freeze/thaw objects.
I for one am disappointed they're using YAML. It's an ugly, non-intuitive (to my non-Pythonized eyes), and obsequiously-different format. But if they do it right, the freeze/thaw layer will be pluggable, so I could use XML, or Lisp, or whatever, as I saw fit.