I recently made a minimal arduino zero board without the debugger. I searched a lot regarding the debugger and apparently Arduino and atmel have closely worked together to create the EDBG interface and is not open for anyone to duplicate.
the arduino bootloader on the SAMD21G18A however can easily be programmed using a raspberry pi 2 and openocd (Don't know if other boards work, I've tried with rpi2 and it works) . Tutorial for that can be found in the following link.