I don't think those are the latest files, are you running the War Begins Beta 11?
If you're not I highly recommend you download it, a lot of new features are present in that beta, like our brand new command panel, new models, the works.
it works very fine. why do you thought it wouldn't work with other mods?
Well, I did wrote those files...
In the latest version I tidied things up and placed all the "extra" files in a folder called includes and then had the skirmisher access those files instead of writing the code directly there, so if the mod you're running is not war begins, the mission type won't find those included files and it'll give you an error.