In Gal Civ III you could upgrade everything on a military ship as long as you weren't changing hull sizes. I haven't found a way to do that in Gal Civ IV. For example if I have an old ship designed with first generation missiles I don't seem to be able to bring it into space dock and upgrade the missiles to Avengers. Am I missing something?
P.S. I just found out this is possible, but very convoluted. Something to do with waypoints. Maybe a better more obvious procedure is in order.