If you can read French, here is an article I wrote some months ago for controlling the build chain (including remote run) using Ant scripts : http://www.pobot.org/Premier-programme- ... r-EV3.html
I prefer Ant based projects since I'm not found of click-based procedures even when working in Eclipse
BTW working with an Ant toolchain makes possible to use lightweight workstations based on RaspberryPi and Geany for workshops I animate for teaching robot programming to college teachers. It's far easier and faster to clone 15 SD cards than to try to install 15 different PCs collected from here and there
If you are interested, drop me an MP and I can send you the build.xml file I use.
Hope this helps.