I found your findings interesting, although I don't use Maven (out of ignorance/lack of time to discover/lack of real need).
Personally, I just went the easy way,
compiling part of Processing on Windows with Eclipse with a little help from a .bat script...
I think that providing a way to use a good, modern tool, independent of IDEs, to do the compilation is interesting. I don't know if fry & al. are interested (I guess fry is taking a well earned break from Processing after making the 1.0.1 release...) but it is probably worth giving your method/files here. Hey, I might even try it!
Trying to answer some questions:
- preproc.pl: I am not a Perl guru, but it looks like it generates the part in PApplet.java that is after the "public functions for processing.core" sentence. That's to make all methods in PGraphics and PImage available directly in PApplet (which cannot inherit from them because it inherits already from Applet). Unless a new method is added (or a signature is changed), no need to touch it.
- apple.jar and QTJava.zip: my guess is that they are closed source files from Apple... QTJava is for supporting QuickTime (the video library).
- examples are reference are probably part of another process.
These are mostly (educated) guesses, I fear... :-D