Most outliners, once you clone an item, will NOT distinguish anymore between the "original" and the "clones", whilst conceptually, there should be an (updatable) difference, and which I call "natural parent" and "adoptive parent" - name it as you like, but it's evident any item in a tree hierarchy should have a "natural/main context", and then, perhaps multiple, "additional contexts" - and be it only for avoidance-of-recursion reasons: btw, I mentioned this problem within a discussion of InfoQube in the outlinerswforum, where the developer of IQ, Pierre Paul Landry, suberbly said (I'm citing from memory), "IQ allows for recursion"... when in fact, recursion is a PROBLEM of IM, and which has to be avoided/contained, and certainly not a feature of IM (development illac ;-) ).
re: natural Parent: Agreed: In InfoQube, an item has a "Main Parent" and any number of other parents. Users can change which item is considered the main parent. The "Main Parent" is used to show hierarchy in grids.
re: Recursion: Why do you see recursion as a problem for IM software. In InfoQube, it is a very useful feature. This ensures that items can be moved around in the hierarchy without limitations (only limitation: an item cannot be a child of itself)