Keeping in mind that these are the steps that Arduino IDE follows when you upload a sketch on the board:
- Merge your sketch with the bootloader
- Program ATMega32u4
We can repeat those steps by hand in this way:
- scp your_sketch.hex firstname.lastname@example.org:/tmp
now let's go in the Yun via ssh to run these commands:
root@Arduino:~# merge-sketch-with-bootloader.lua /tmp/your_sketch.hex
root@Arduino:~# run-avrdude /tmp/your_sketch.hex
avrdude: verifying ...
avrdude: 12866 bytes of flash verified
avrdude: safemode: Fuses OK
avrdude done. Thank you.
Ah... if you are wondering: "Where is the hex file of my compiled sketch?" then go to the IDE preferences and enable the verbose output option ;)