gdb along with a debug server from OpenOCD or JLink or whatever. Assuming the MCU has the proper debugging support. This works well on the Cortex-M0 at least (t

gdb along with a debug server from OpenOCD or JLink or whatever. Assuming the MCU has the proper debugging support. This works well on the Cortex-M0 at least (the annoying thing is you often have to switch between the bootloader .elf and the application .elf).