Apparently I missed some important information somewhere. I've been expecting to run into information in the game in how to obtain Intelligence, Pilot or Command BOffs beyond white quality, but it isn't happening. I did manage to get a token once to convert a BOff into a pilot some time back, but it's character bound to my main character, who specializes in Intelligence, and has no use for a pilot. I have no idea how to get any more such tokens, or find a high quality Intelligence/Pilot/Command BOff.
Any clues for clueless people such as myself?
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Once you have a manual on hand the ability to add it to your Boff is on the top of their skill page.
Specialization manuals are not bound, and are sold on the Exchange.
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The career (Engineer, Science, Tactical) can't be changed.
Multiple specializations can be learned, but only one can be used at a time.
Specialization seats on T6 ships are usually something like Sci/Pilot or Tac/Intel or Uni/Command, or whatever variation your particular T6 ship happens to have. So you have to match both the career and the specialization to that seat.
In order to teach a specialization to a bridge officer, you need a Specialization Qualification. You can craft them yourself if you've got ten points in that specialization, or you can buy them off the exchange for a few 100K EC (search for Specialization Qualification - Pilot, for example) - they're UR quality, if that helps narrow it down. Once your bridge officer has learned a Specialization, you can go to the bridge officer trainer and buy the Rank I and Rank II skill books for that specialization and teach them to your BOff (they learn a mix of skills from the qualification as well). Rank III books can be crafted if you have a high enough rank in the specialization yourself, or bought from the exchange.
It's not a terribly complex process (if a bit opaque) once you get the steps down, but it requires a bit of running around ESD or FC to get all the bits and bobs you need, unless you're flush and just want to buy everything from the exchange. Hope this helps outline all the steps needed. Feel free to ask if you have any other questions.