I can tell you how we do it on our systems, and hopefully it’ll be relatively straightforward to translate to your debug environment.
We use the stlink command line interface:
Once I’ve got the Core hooked up through the ST-Link/v2 programmer and in bootloader mode (flashing yellow), I would open one terminal window, and then type st-util -p 9025, which opens a gdb port.
Next, I would open another terminal window, browse to my build directory, and run arm-none-eabi-gdb core-firmware.elf. Then within the gdb console:
target extended :9025
kill
load
run