... 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.