The Arma 3 Launcher has support for modpacks that are on steam. As far as I'm aware this is what's going to be used and it should be as simple as one click and wait to download all of the mods.
And as for the mission file, I'm not so sure. I don't see that being possible, and even if it was in the mission file it would have to be mods that would require a tiny amount of space ie a few megabytes, instead of maps, vehicles and weapons packs which can be gigabytes in size.