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