There is a solution for your problem , however some corners have not been detailed enough. For example , what if there are 2 files , one in D1 and one in D2 , and they don't sit in the same place ( relative to D1 and D2 ) but they have the same content . Would that be considered a duplicate or not ?
If the answer to that question is no then you can use shlomif's nice method for recursive diff of 2 directories found here and tailor that to your needs.
Otherwise , it may be more difficult and you might need to calculate some hashes for all files(in both D1 and D2) and start seeing if the files have been included before in Dd or not.
