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For debugging to work I would need to use the Optiboot bootloader and use FLASH breakpoints as per this explanation.
On the official GitHub there is an Optiboot version of the bootloader for use with the Controllino MINI. Sadly, however my project requires a Controllino MEGA and for this only the standard bootloader seems to be publicly available.
PlatformIO together with avr-stub can be used to do source level debugging but there are some caveats.
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