Hi!
I've just published my latest project... the idea came from a post by Federico that explained what happened when the IDE uploads a sketch to an Arduino Yun.
I developed a webapp (using PHP) that allows to upload sketches (well, the compiled version of them) on the ATMega32u4:
http://www.lucadentella.it/2014/02/10/yun-sketch-uploader/
(english version available too!)
I found it very useful to update a couple of Yun I left in different locations and connected to the Internet... the webapp is password-protected so no one but you should be able to use it!
Thanks