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I think it's more than possible that files uploaded from different projects could collide and eventually start to cause problems overlapping each other.
perhaps each "folder" should have a base location that starts with it's group name, which obviously can't collide with another which has the same name, so then you'd "namespace" all the files automatically so they would only collide with files within the same project, existing in the same folder. which is obviously then a normal file management problem.
the problem is magnified by what seems to happen when you put files inside folders, they keep their original name....hmmm, not sure about this, perhaps it's just my mis-interpretation and I hope somebody can tell me that it is.