Software directory is used *ONLY* by MESSUI Picker. It is a shortcut for the command line fullpath loading. I.e. if you have a piece of software in C:\mysoft\system\game.bin
you can either launch by command line with fullpath by typing (assuming game.bin is a cart)
mess system -cart C:\mysoft\system\game.bin
or setup in MESSUI the software directory for 'system' to be 'C:\mysoft\system\'. In the latter case, the MESSUI picker will present you game.bin (and the other files contained in C:\mysoft\system\) in the Picker tab, so that you can launch them by double clicking on the single files
THIS DOES NOT APPLY TO SOFTLISTS 
It is only for usage with MESSUI and the picker (and indeed command line MESS does not use the software folder at all)
OTOH, roms/ (or any other rompath of your choice) is used to store bios files *AND* folders with software list sets. If you put, say, x68_flop/ files in a directory which is not set up as roms directory, MESS won't be able to load x68k disks through software lists. If you put it in the roms/ folder, MESS will launch it from the Software List tab.
Final remark: software list sets are expected *NOT TO WORK* with the picker. if they are floppies or tapes, they could work, but if they are carts they often won't work when loaded through the picker. so the difference between roms/ and software/ is important
Anyway, since there seems to be confusion on the subject, I will try to update the manual next week (when I'm back from a work trip) with detailed explanation about this. The software folder is currently not well described because it is a MESSUI only thing and I use MacOSX so I focused my attention on the Command Line... I will rectify this soonish 
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