Is there a guide somewhere on maximizing shipyard performance? Retooling, refitting, and "secondary classes" are all a bit hazy for me; my shipyards are constantly retooling, and I know that wastes a lot of resources and time.
If you are constantly retooling then you either have too many classes per shipyard or not enough shipyards per class.
Looks same but it's not.
Too many classes per shipyard meaning you may have some ships which could serve the same role bringing down the classes needed from let's say 3 to 1 and consequentially you will end up needing fewer Shipyards. For instance, having GEO and GRAV together already reduce classes from 2 to 1 or explorer with GEO and GRAV from 3 to 1.
Not enough shipyards per class meaning that if you do have 10 active designs, you ideally want to have 10 shipyards tooled for purpose. The one ship that you are planning to build only once could be done under a "service" shipyard which will be mostly retooling every now and then while the others will retool only when a class is being updated. Usually, such shipyard has only 2 or 3 slipways.
In my opinion some retooling it's still organic and should be taken into account.