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I have no idea how it works, and there is pretty much no info (that I can find anyway).
Is it worth building rep, what does it really do? I have no clue. The feds caught me smuggling once and they have been hostile with me since Gamma. On the other hand, this seems to have no affect on me whatsoever. If I wanted to fix it, I'd have no idea what to do. I built up pretty good reputation with a federation member corp, but this seems to have no affect on the feds opinion of me.
Also, I really haven't figured out how to make a lot of money yet. I have gotten my Cobra, but the economy seems pretty weak pretty much everywhere, so my profits aren't scaling up very nicely. I did get one transport mission with a huge payout (it was clearly because I had good rep, but it also seems to be very, very rare), but for the most part the only thing that makes a lot of cash right now is trading. So another question is, will building rep help me to make more money?