If you look at the Download page on this site, there is a link to the source that downloads arduino-1.0.1-src.tar.gz; I did this to my Windows machine. Looking at what is included, there is only the Linux directory in the arduino-1.0.1\app\src\processing\app directory. Windows and Mac are missing.
I got them from GitHub. They should be included, or the page updated to state the source is Linux only
Interesting. Does it compile?
The real place to download the source is here:
... Download page... Windows... I got them from GitHub... ?? It's the instructions on this site that I was highlighting
I was interested in the IDE interface for editing (not compiling) the sketch, so loaded it into NetBeans. Setting a few file locations, I got it to build and run (and debug) in NetBeans. I need to do a bit more work to check if it runs as a stand-alone jar file (and lots of testing).
I have cloned the repository (in NetBeans) from git://github.com/arduino/Arduino.git but only picked the master branch. There are a few other branches, but I don't know what they are for.