I have a plethora of downloaded documentation and have yet to get a handle on the firmware itself.
Can the firmware be completely rebuilt from the arduino package?
I would like to make some major modifications to my quadcopter (APM 2.6) and some of the modifications might be be better employed as a modification of the firmware rather than just adding more programming that occasionally ends up fighting the firmware.
yes of course, just like any thing else that is open sourced and/or shared in a Git repo. If you don't know how to build software or firmware from source though. I would strongly urge you to take some time to polish your skills before making "major modifications". In any event, good luck.