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The bootloader program is always present in non-volatile memory of the microcontroller. This means that after programming the user's program, there are altogether two programs present. Both programs need to be able to activate each other and they typically share resources such as the interrupt vector table.
How this is handled by both the bootloader and the user's program for a specific port is described in this part of the manual.
Note that the OpenBLT bootloader includes a microcontroller port template. Using this template as a starting point you can easily add support for a new microcontroller family yourself. Refer to this blog article for more details.