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You can use C++ with c4ev3, also available as Eclipse Plugin. If you are ok with sending the commands remotely, you can even use any language that supports popen() like functionality, (which includes every useful language out there, with some bash-fu even Brainfuck). Check out moveEv3.pl.
c4ev3 has an Eclipse CDT Plugin based on GNUARMEclipse so you can do your C/C++ Programming for the EV3 and upload/browse the filesystem without leaving Eclipse. It works with the stock firmware/OS and comes with an API to access sensors/motors. You can run it on Windows, Linux and OS X. Also compiles on FreeBSD but didn't test if it actually works. If ...
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