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If it's like the miniscule bit of C I poked around with years ago, those open up the specified terms for use later in the program. If you omit those lines, then any processing that tries to use those terms might break.
I know next to nothing about this, but it occurs to me you might be able to change the moves / weapons / whatnot of the shipyards in their defs file so that they could function like a more regular starship? Might never be able to adjust/evolve them though, but if you're content with having a uniform hive-ship it might work. Or to say it another way: It might work better to make a shipyard with starship functionality than make a starship with shipyard functionality.</p
Caveat: I just got the game yesterday so might be on the wrong page from what you're looking for. In the process of learning about the game, I found GamePedia pages that sound like what you may be looking for: Races: <a href="http://galciv3.gamepedia.com/Major_races" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://galciv3.gamepedia.com/Major_races&source=gmail&ust=1466865030946000&usg=AFQjCNE1SN