I am attempting to migrate a project currently running with makefiles in Atmel Studio to CLion, with an Atmel SAM-ICE branded J-Link device. With the "Embedded GDB Server" configuration in CLion I can start the server and connect to the device and debug a device programmed through Atmel Studio. However I have limited success programming the device from CLion, since I need to flash two elf files: A bootloader (Debug information not required) and the main application (Debug information required), …