Would it be possible to make a new "flagshipCapitalshipyard"? This would solve the problem with your first Capital being free.
Hey SuperZERO, to my knowledge there are a fixed number of ways to create ships: Frigate Factory, Capital Ship Factory, StarBase, createFrigate ability and spawnShips ability. I don't believe it's possible to create a new shipyard that wouldn't have to use an ability to spawn ships.
The problem with using abilities to spawn a capital ship is they don't follow supply lines correctly. For example: spawnShips will spawn a capital ship but will ignore the capital ship supply availability. I did one test where I spawned 50 capital ships, lol.
You could use the existing model and textures to save on memory and such, perhaps make it research-able.
I do plan to use the existnig textures and will only have to create new meshes for resizing which shouldn't be too bad.
I think your mod is already great for a researchable capital ship so I'm just trying something different here to see how it plays out.