The Arduino Zero Eagle schematic and board files are now available from the Zero's product page: https://www.arduino.cc/en/Main/ArduinoBoardZero
By the way, there's a mistake in this new Eagle schematic.
Digital pins D2 and D4 should be swapped:
D2 should be connected to PA14 (not PA8).
D4 should be connected to PA8 (not PA14).