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Ok. I set some neutral houses, four of them
You're talking about a Multiplayer map, right? You can't make custom houses on multi-player maps. Though I've never tried making secondary civilian houses in multiplayer maps.
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I have set a trigger "Make Allie" that will start to wqork when teams build certain buildings.
This trigger will only work correctly if certain players have a certain house color. This technique is reall bugged in FinalSun, as the only preferences you can set are Nod and GDI (Playable houses), so the Nod Player who's red will be the only Nod player who'll get the effects of this trigger, the same applies for GDI, but Gold instead of Red.