How can I make Game Maker run other programs through command lines?

[TheShyGuy]

Did you take a look at the link? A quick skim shows that you can set the set characters + stage from the command line.

I'm not sure how to check when MUGEN closes, unless it outputs to the console before it does. You'll have to do more research on that. You should be able to close MUGEN when GM closes, but again, you have to research that and I'm sure you'll find useful info.

Why do you need to modify a program through a Hex editor? Just find any Hex editor, open the file, and edit (as long as you know what you're doing)