During the game (not on the title screen) you can press F4 to toggle full screen. Does that help?
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Thanks for letting me know. I released a small update which I think should help. I could just prevent spawning into other ships but I think it's kind of interesting that it can happen, it seems realistic.
As far as weapons there are just swords for short range and missiles for long range, although you can improve them by putting the energy parts next to them.