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Since I think Good Old Games, Wine and PlayOnLinux is the perfect combination, I have started writing POL-scripts for my games from GOG. Quite a few of these are packaged with dosbox. The GOG-installer does a pretty good job of creating nice shortcuts on the desktop (and in the menu) to the games, but of course wraps them through wine + dosbox. Like this:
env WINEPREFIX="/home/gabriel/.PlayOnLinux/wineprefix/SpaceQuestI-III" wine C:\\\\windows\\\\command\\\\start.exe /Unix /home/gabriel/.PlayOnLinux/wineprefix/SpaceQuestI-III/dosdevices/c:/users/Public/Skrivbord/Space\\ Quest\\ 2\\ -\\ Vohaul\\'s\\ Revenge\\ and\\ Space\\ Quest.lnk
With a bit of script-fu I can find the ".desktop"-file and menu entry and fix this to use the native dosbox instead and all is well.

My question is:
This solution is only valid in a freedesktop-compatible environment (I think). Is there a better way of doing this which would make it work in MacOSX or FreeBSD? Or am I being to ambitious? ;-)

Hey.
I cant answer you question, bu I will be very happy if you share some of your commands. I just bought Duke 3D, and saw it was packed through dosbox. Just one command, that makes the command start with native dosbox :)
BTW, dosbox crasheh under wine for me