Mandatory Hardware not showing

When I have my pixhawk attached to my macbook pro, I can "Connect" in the upper right hand corner of APM Planner. If I then go to Initial Setup, "Mandatory Hardware" is not showing. 

I have the 3DR GPS, 3DR radio, Transmitter, power module and ESC con

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Will the Pixhawk firmware be different than the PX4/Firmware on Github?

At http://copter.ardupilot.com/wiki/common-pixhawk-overview/ I read:

The Pixhawk is still getting the final polish on it’s firmware and will have a lot of room for future firmware enhancements.

Does this mean that https://github.com/PX4/Firmware will n

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