http://mamedev.emulab.it/clrmamepro/binaries/cmp20141211.rarnow with %f\%1 as default naming which mean set subfolders...hurray ;-)
...and a "profiler options" option to select how many files get renamed....
- single file ...only renames the clone file with a hash collision
- single clone ... all files within this clone
- all clones ... all files in all clones of the currently affected parent/clone relationsship
(this option aren't used when you turn on the hash collision full merge mode....but that's a different story..)
default is sinlge file for now to achieve less renames as possible...and with subfolders you don't really have renames anyway...
Such options can be switched without restarting cmpro/reloading profile.....also merge modes can be switched as you like..
happy testing ;-)