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but not been able to add any new ones using existing templates.
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You should not have had a problem with this, I have successfully added new ships with no problem at all.
http://img688.imageshack.us/img688/9653/starwolves3.jpg
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It doesn't show up in the shops unfortunately. And as of yet I can't figure out why.
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Either you did not add it into the file properly, or you simply were not lucky. Remember that a shop does not display all of its inventory, only that which passes the random generator.