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Is it possible to use a custom bootloader, that loads and executes a main program which is stored for example on SD-card? The idea is to make it possible to update the Arduino remotely.

I tried this with a bootloader, that writes the program into the flash storage with a 32KiB offset and then uses a function pointer with that address (0x88000) to continue execution there. (The 0x80000 is as far as I am informed the address offset of the flash storage.) It can be written on Due boards with this library: https://github.com/sebnil/DueFlashStorage. The problem was that this just hasn't worked, the Arduino simply stopped responding after the function pointer being executed. I would appreciate any information or hints on this topic.

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Not sure if you could get the bootloader to support SD, but i have little experience with bootloader code, so it the way i would go about it would be to make the sketch load content from the SD that then effects the sketch process.

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