The Arduino package contains an IDE that can be used to develop and upload code to the micro-controller. A current arduino package is available in the repositories of most Linux distributions (Ubuntu and Fedora, anyway). But sometimes, you need to use a different version of Arduino for a certain use case. For example, the distro doesn't have the most current version that you need to drive your new-fangled dev board from Adafruit or PJRC. Or, the new Arduino package breaks your existing code or compatibility with a different device.

You can use the Adafruit ATMega32u4 breakout board  as an Arduino Leonardo by flashing the bootloader in Arduino 1.0.1 to the board. To follow this process, you use another Arduino, like the Arduino Duemilanove, as a programmer.