Re: Building Harmony Based Boot Loaders
The bootloader linker uses bootflash, and puts interrupt vector tables there, etc. The standard linker puts it there too. So you have to use a different application linker so they don't overlap. Nkurzman's first answer really is correct here, but it may take a bit to digest this.
Do you have a clear concept of what the linker script does?
To combine into a single hex file, you pretty much just need to add the bootloader project to your application project. Project->Properties->Loading. If you get any linker warnings after doing this, don't ignore them.