|Arduino Java Based IDE|
Peeling away the surface of Arduino reveals that it is just a set of electronic components based on a microcontroller (which one depends on the Arduino model). There already exists software development and programming tools for these chips, often made available free by the chip vendor. So, the solution is to get a hold of these tools. For the Arduino API, since it is open source, the Arduino folks make the code available for free as well (it comes with each release of the Arduino software).
|AVR Studio IDE|
Where I am at now is, I managed to port my "engine room lighting application" project from the Arduino IDE to the AVRStudio IDE. Now I can more easily code and debug C/C++ code to control the device. Woo hoo!