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Technically, dig in to the code to learn how it is built, debugged and run. Know about all the configuration items. Find all the big pieces in its hierarchy of objects. Some of them are important to know well. Others it is important to know of their existence. Some you can just be marginally aware of. Any that deal with subsystems, creating visual elements, communication between subsystems or keeping things running correctly from cycle to cycle are important. Fine details can wait till later.
http://wiki.flightgear.org/User:Callahanp/fg-from-scratch Callahanp - Flightgear From Scratch]
[http://wiki.flightgear.org/User:Callahanp/Flightgear_Technical_Manual Callahanp - Flightgear Technical Manual]