The debug port is a SWD port (same as on Arduino Zero). You can use for example an Atmel ICE debugger to connect to it.
The Arduino IDE currently doesn't support any debugging modes, only programming of sketches and bootloader via the SWD port. Atmel Studio does support debuggin the Arduino Zero so it should be a small effort to get the Industruino D21G supported in Atmel studio. We will look into it.
Schematic can be found at the bottom of the D21G topboard product page. Here's a direct link to the schematic
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