Note that your usage (cp -a D[12]/* Dd/) will take the "depth 1" contents in ascii-betic order, and deeper contents in "arbitrary" (directory content) order, so in any case, file age doesn't enter into the logic.

If there might be path/name collisions among the source directories, where differences of age and content matter, you might look at "rsync" (for which you'll find perl modules on CPAN, in case that helps, but you'll probably need to grok the rsync command-line tool options anyway, so try "man rsync").

My thoughts upon reading this (which I hope would prove helpful) were :

1. Use File::Find to generate a list of files (also potentially at this point exiting or asking for processing options for duplicate file names)
2. Use the -d dirname test, mkdir() and File::Spec to create subdirectories that may be needed
3. Use File::Copy's copy() function for the final movement

At least, that's the process I would likely procede with (assuming a better solution were not proposed).

HTH.

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.