Not sure if this would be completely viable but I figure it may be an interesting way to approach mods. They would still function normally within the game. Though I think it might break load order mods, since it may be dpeendant on file time, though I have not fully investigated this.
I know this system is used for Garry's Mod (Half-Life 2 mod) and stuff from other games doesn't always work for others but I figure it could be a suggestion, at least for large complex mods.
Thoughts?