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If I do ever find out what I did to make the houses allie with the different players, this will be the first place I post it. Or maybe not. Now thinking about it, I wish I had told you earlyer...
I've already began looking in FinalSun to find out what would be a good technique of getting this working to a reasonable extent. My attempts just turn out to be worthless, as because of what I said earlier: It's not possible to add custom Houses in Multi-player maps.
Anyway, It's not possible In TS / FS Multi-player maps, and Unfortunatly, that's not going to change unless someone does some miracle patch work.
But yeah. Keep In touch, I'd like to see your work.