If you’re looking for a quick answer, its that these two just don’t work together. However, the Yun is still a great product that’s well worth using and there are ways to get around some of it’s limitations.
The Yun combines a newer, higher end Arduino microcontroller with a small chip running Linino, a variant of the OpenWRT Linux distro. To that, they’ve added a micro SD card reader, an ethernet port, and a WiFi antenna. This combination lets you easily interface hardware with online API calls. it’d be great to use Git to manage code and other scripts on the Linux distro, but its limited nature makes that difficult.