Right now it's arduino based. We are thinking about possibilities to separate us from that build environment, because it's so weird..
The only problem is that arduino is so popular with newcomers to programming and hardware, and for them it's relatively easy to use. It's only the more seasoned developers that knows something better is out there, that complains
I still use the arduino environment for the basic sketches, as it kind of works, and atom for core hacking. I've got a set of bash scripts to help me along, and use gdb for debugging in target (samd hw)
I think there are some platform.io integrations as well, but haven't had the time to look into that. We want to reach out to as many as possible, and that's with arduino at the moment.