I've been working for a while now on my own runtime library for AVR microcontrollers (developed mostly on Arduino & clones).
It is written in C++, and is suitable for those wishing to code directly, rather than through the Arduino. I use Eclipse myself, and found it quite suitable (although there is a slight learning curve, and a lot of plugins to play with). The library is shipped as an Eclipse project, but also include Makefiles that will build with a small amount of massaging.
The design philosophy was efficiency rather than hand-holding, so things are a little verbose in places. Where possible, this has been hidden in macros. The benefit of this is far more control is handed to the user via the runtime, without having to fiddle with the hardware directly.
Theres still lots of work to do, so if you want to contribute, please ping me with what you would like to work on, and I'll do my best to help you get settled in.
Full information, git repository & tarballs are available at:http://www.makehackvoid.com/mhvlib