Remotely upload sketch to Arduino Yun using command line.

1. Compile and get the hex file
   
   In Arduino IDE,
    -  Sketch > Export Compiled Binary
       Wait for the compilation process to finish
    -  Sketch > Show Sketch Folder
       Let's take the one without bootloader.
    
2. Copy [your_sketch].hex to the Yun You@PC $ scp [your_sketch].hex root@arduino.local:/tmp
3. SSH into Yun You@PC $ ssh root@arduino.local
4. Merge your sketch with the bootloader (for the one without bootloader) root@Arduino:~# merge-sketch-with-bootloader.lua /tmp/[your_sketch].hex
5. Program the MCU (ATMega32u4) root@Arduino:~# run-avrdude /tmp/[your_sketch].hex Done!