YUN. How to reset the micro controller from linux? As the title, I'd like to reset the Arduino sketch from the linux machine. Is it possible? how?

One solution could be to save the hex file inside the sd card and then upload it via the lua sketch but I think there is a smarter solution.
According to the Yun schematic, GPIO18 of the SoC is connected to the MCU reset circuitry. Toggling it should allow you to reset the MCU.