Upload sketches to an Arduino Yun via command line

1. compile sketch via IDE, find the hex file belonging to that compile in IDE log 
2. copy that to your Yun (SCP, FTP, WinSCP, ....)
3. ssh to your Yun and do:

 /usr/bin/merge-sketch-with-bootloader.lua  /tmp/mysketch.cpp.hex
/usr/bin/run-avrdude    /tmp/mysketch.cpp.hex

Now you have your sketch on your Yun.
You do not have to be in the same LAN, you can update via the Internet as long as you have access to you command line.