Missile turrets (i.e. installed on mothership) were actually already designed (see "LRM2_GK" definition in Modules.xml) - the only thing missing is the "on/off" toggle for missiles on mothership.

Note: I haven't actually tried attaching a missile slot to big ships; I'm just taking the word of those who have.

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Active perks are also unavailable to pilot sitting in mothership slot. I suppose some of them can be ridiculous (imagine using the increased speed piloting perk while flying the Astartes...), but if they just added a tag on each perk to indicate whether the perk is allowed on mothership or not - similar to Modules_xml "attach_type" - that would solve the problem.

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Passive perk behaviour appears to be hardcoded inside perkDispatcher.script and CalculatePilotSkills.script. Would it be possible to make perk behaviour depend on the actual definitions inside an XML file, like how modules are currently defined? You would have to modify the two perk scripts extensively though, to loop through each pilot's perks and check whether it contains the tags a function is looking for instead of using hardcoded pilot:HavePerk() checks.