I want to flash a hex file stored in a micro SD card into an Arduino [Uno/Nano]. So far I can read and write to the SD card using Arduino.
Without modifying the bootloader, is it possible to flash the Arduino using micro SD card module?
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Yes, but I am not sure it can work from the smaller Arduino models. Have a look at the Phoenard project. The platform, based on a 2560, flashes .hex files on demand, which are stored on the SD card.
It's an open-source project, so it should be possible to go through the code and see how they do it.