Intel provides an IoT version of their sdk for C/C++. I can say that none of my development is via Arduino.
I have the mini break outboard, Linux booted, ssh into console and develop in Kylix3 (pascal) or gcc C/C++ (onboard), so I can choose to use or not use the IDE.
Python is also onboard.
Pin programming is available via libmraa.
arduino sketches can be removed located at /sketch/sketch.elf and the loader can also be disabled using systemctl.
Your options are flexible, and you can use sketches, packages and your own Linux programming in any combination you see fit.
Thanks Deium. You mentioned a systemctl command to disable the sketch loader. What is it?
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systemctl stop clloader
systemctl disable clloader
I found out you have to have 7-15V at the power plug. With 5V, Edison will simply loop.