The flashing is done thusly:Upload a sketch to Arduino directly from Linino - #2 by federicofissore - Arduino Yún - Arduino Forum
Judging from the tools available on the yun the IDE likely uses scp to transfer the compiled sketch.
For a really circuitous setup you could Flashing other Arduinos with a Yun - Arduino Yún - Arduino Forum if you plug a USB cable from the USB A to microUSB B and power the Yun with REGULATED 5 volts from somewhere else. I haven't tried this, it would be a very good idea to check the schematics to make sure the Yun wouldn't be damaged by trying to power itself from one USB to the other. Since that post I have been using openssh-sftp-server - 6.2p2-1 from http://downloads.openwrt.org/snapshots/trunk/ar71xx/packages/ instead of pure-ftpd.