The problem is not trees, they are readily available in many formats. The problem is schemas. If there are no rules on the branches everything becomes "Old_stuff" or "important_work" or whatever people do to their document folders as the tide turns.
You need trees layered over trees to provide some structure and get that sweet workflow QC. Graph-homomorphisms between trees that is, or slice categories over whatever structure you need to maintain. Trees (or graphs) in semantic/syntactic relationships stacked as high as you can muster. Usually this is presented as a two-layered structure-tree+data-tree system in end user applications, with a fixed semantic tree depending on the domain in application. The trick is finding the balance between end-user configurability of layers n+1 and the required knowledge to design useful structures. People who edit layer 2 should probably be domain experts, and layers 3 and above are best left to programmers and computer scientists. If this was a solved problem, nobody would buy CRUD-software, and a good half of us would be looking for work.