The folder doc/ contains this documentation, the schematic files (schematic.sch created with CADsoft Eagle and exported to .png), and a PDF file with the HID specification which contains the HID keycode table.
The folder keyboard/ contains the main Arduino program. It has a main loop which reads input pins and writes them on the serial port to the custom keyboard firmware. One thing to note here: the READMASK constant defines a bitmap mask which defines which 5 input pins (numbers 2 to 7!!) to read. For the 2-button controller shield, set this value to 5 to only read pins 2 and 4; for the joystick+button shield, set this value to 31, to read all inputs from 2 up to 7.
The folder keyboard-firmware/ contains the firmware for the Arduino UNO which allows it to act as a USB keyboard. It requires the LUFA library (version 110528). Source code was originally taken from this page and then adapted to work with a more recent LUFA.