There are a whole lot of references to compiling Java code. Is there a reason for this?
This is because the Arduino IDE is based on "Processing" ( http://Processing.org ), a "simplified" programming system for the desktop. Processing has similar principles, but creates "mostly java" code, where Arduino (or "Wiring") generates mostly C++ code. The pieces of the IDE that would have compiled and run the Java "sketches" of Processing are replaced with pieces that preprocess, compile, and upload, the avr-gcc code of Arduino.
PS: a questioned "to be answered" is whether modifications to the Arduino IDE will be accepted at all, or whether it's more efficient to stay in sync with the Processing project...