What methods are there in Star Marine for marking rooms, like dropping green flares? If you're working from one end of an Idris to the other, are there tools in place so that you can mark a room as clear for fire teams to work their way through?

As of now, no. That doesn't seem like that would be difficult. If you had a flare item, you could have flares, or obviously you can be ting "Clear this room" or whatever to your teammates. But in the first FPS, there's a set of gadgets that you can deploy. So things like a hologram gadget, a shield gadget, area denial systems and stuff like that. But we don't have a marker for the FPS, although it's not a bad idea at all. And it wouldn't be particularly difficult to do.