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.