In the Shipyards there is a button to "upgrade to current design" but this button only works with the stock game designed ships.
If I design a new ship and name it Killer.. and then get better engines so I go and select Killer and redesign it to have the better engines and then name it Killer MK1 or something... there is no way to designate in game that this is an upgraded ship.
So all of my shipyards then have to be touched to stop building Killer and start building Killer Mk1
This could be fixed with the current automation that is currently in the game if the "use this design" was replaced with an UPGRADE button...
