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Debugging with a bootloader

I have written a bootloader for a cortex-M1 processor that starts at 0x0. It correctly loads the code I have stored in a serial flash chip to RAM starting at 0x60000000. I can successfully go through the debugger with this project and then when I jump to my other projects reset vector I can correctly go through the assembly.

However, I do not want to go through the assembly of my main application I want to debug it like a normal project. What is the best way to do this?

Right now I have two separate projects with each having their own main.c files. If I have to combine the projects, what is the best way to do that?

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