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Thank you for the hints...with complicated, I just meant, I spent hours in the internet to find out in principle what to do. I know Arduino aims more on beginners than on hackers, but nevertheless, Arduino is usable for serious applications. And watchdog is missing in the libraries.There are other AVR mega chip built-in hardware functions that are not directly supported by the Arduino core libraries. The watchdog is just one of them. Sleep modes, pin change interrupts and others are not directly supported but has had many request to do so. This doesn't prevent a true hacker from accessing them if they study the AVR datasheet and read the existing arduino source code.
Main thing is, I agree, to install the proper bootloader. Why does the pre-installed bootloader not deactivate the watchdog? This should not really be a technical problem, is it?
Because the Arduino core libraries did not use or support WDT functions they saw no need to disable WDT interrupts as part of the bootloader start-up code. Others saw the flaw early on and had posted patched bootloader, such as ADAFRUIT, and made it available for downloading directly to users. The Arduino Co. was slow or reluctant to make the change, and I have no memory of the exact status of current arduino shipping bootloaders are at. I think Uno bootloader supports WDT, but Mega boards still do not?
Anyway, do you have a link to a bootloader that officially supports Arduino Sketches on a Mega 2560? Sorry if this is a silly question, but I have no special knowledge which bootloaders are available and which one to use for which application.
I don't have a link but I pretty sure there is a newer mega2650 bootloader available somewhere that handles the WDT correctly and fixes the !!! bootloader monitor problem.