Maybe I misunderstood, but there is one thing I don't like very much about it is the 'shipyard.lua.1' 'shipyard.lua.2' because that would mean that mods still need to make the file names unique between mods.
If I can suggest I would like to see each mod having its own folder with similar folder structure as game and the game automatically loading scripts just as you described but from mod folders. That way the mod can still call the file 'shipyard.lua'.
This way each mod will have its own directory that can contain even other content, like textures, sounds etc and it will be easy to manage.
I know that it may be a bit more work, but in my opinion it would be worth it.
Otherwise it sounds great, it's definitely better than what we have now :)