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This should be possible, sharing functions or interrupts between a custom boot loader and application is possible as long as the address is known to both. What is happening in the application when the UART interrupt should be firing instead?
Is your UART interrupt able to function for your application without the use of variables that are local to your boot loader?
If you want to look at another potential implementation, inMSP_BOOT,the application vector table is redirected to from the vector table in the boot loader memory space.
