hey there, I was told that there is an increasing demand for an Atmel Studio alternative for linux.
Well I've been developing one for the past year or so and I think it is now polished and ready to be used, bare in mind though that it is not as professional as Atmel Studio's IDE, but it gets the job done. I've tested it on Ubuntu 14.04, though any debian distro should work, and windows and it works fine.
here's a link to the github repository:
feel free to contact me if there are any issues.