Yes this is a common question.
Generally we would like to support common subtree elimination.
For example if one has multiple backups and would like to merge them you could:

  1. Rather than selecting a list of dirs to search, you select input dirs to merge, 
     with up/down buttons in the dir list, which would define the priority for dirs
to keep.
    Would definitely need to auto delete empty dirs when doing this merge.
  2. detect duplicates and delete all in other dirs while ensuring 1 left in each group
  3. mv or cp other dirs structures to keep structures (using tar/rsync?)

If the dirs have different structures then I suppose we could md5sum the list of
md5sums in a directory, for a more general solution.

more thinking required...