Yes, I am sure you have noticed that NuttX is provided as two tarballs: One called nuttx-a.b.tar.gz that hold the core OS functionality in the nuttx/ directory and one called apps-a.b.tar.gz that holds sample application code in the apps/. That apps/ directory is meant to be a "break-away." You would discard the current apps/ directory (taking whatever is useful to you), and create your own application directory.
Note that our "App" is more than a userspace "app"
It's also a FIQ interrupt handler and some 'drivers' (for the GSM specific stuff like DSP / TPU and the RF / external chips). I'm also leaning toward having the board definition separate (at least part of them) since they'll including things like RFFE stuff that will only be useful for the GSM stuff.
Cheers,
Sylvain