PlatformIO and their Atom based IDE might be a good alternative for people that don't want to move to the Arduino IDE or want more support for different development boards.
I've recently started to use PlatformIO after starting a project where I have an Arduino connected to a Raspberry Pi. The rpi is headless, and the Arduino IDE will not work without X running (the hacks they suggested didn't work out for me), PlatformIO has a great command line base that is working great for my use case, flashy lights! https://youtu.be/ww1q248jc7Q