On the A1U eval board, there is a target USB and a debug USB. I was wondering if it was possible to keep this feature (the debug USB) when moving over to a pcb. I've read a bit into it, and it looks like it's just a few pins mapped to a USB port, but I am probably way off.
awneil 
the A1U eval board
You mean the XMEGA A1U Xplained Pro Evaluation Kit;
Part Number: ATXMEGAA1U-XPRO
http://www.microchip.com/DevelopmentTools/ProductDetails.aspx?PartNO=atxmegaa1u-xpro
I was wondering if it was possible to keep this feature (the debug USB) when moving over to a pcb
I don't think you can buy the EDBG chip anyhow, but why would you want to do this?
it looks like it's just a few pins mapped to a USB port, but I am probably way off
No: it is a second microcontroller - effectively, an Atmel-ICE built onto the PCB.
See section 3.1. Embedded Debugger in the User Guide: http://ww1.microchip.com/downloads/en/DeviceDoc/Atmel-42211-XMEGA-A1U-Xplained-Pro_User-Guide.pdf
Again, why would you want to include that in a final product??
EDIT
typo
USB debug can be very useful on production hardware. Techs in the field can get diagnostic data out, load diagnostic firmware etc. No need for a bootloader, firmware update can't really fail as you can always retry with a built in programmer.
clawson 
I don't think you can buy the EDBG chip anyhow,
awneil USB debug can be very useful on production hardware.
But I still don't see the point of putting, effectively, a full AtmelICE into the shipping product.
The usual approach would be to provide the debug header, so the "Techs in the field" can apply their AtmelICE ...
awneil people would be under-cutting Atmel-ICE sales right left and centre?
I wonder why nobody does that - especially considering the cheap ST-Link knock-offs you can buy on ebay, et al ...
(and a genuine ST-Link is only about twenty quid anyhow).
Did Atmel really manage to secure their EDBG so much better than ST ?
I thought that the EDBG chip was just an ordinary Atmel MCU, maybe a AT32UC3A4256.
If that is the case then cloning it shouldn't be difficult.
gchapman I was wondering if it was possible to keep this feature (the debug USB) when moving over to a pcb.
MattairTech
Development Boards
MT-X1S ATxmega128a1u USB development board
...
Revision B now available!
...
USB can now connect directly to the XMEGA USB pins....
The XMEGA can be programmed over USB using the optional onboard AVRISP mkII compatible PDI programmer.
...
Debug over PDI is proprietary though can be decoded:
https://sigrok.org/wiki/Protocol_decoder:Avr_pdi
Program over PDI is in the datasheet.
Edit: sigrok
clawson If that is the case then cloning it shouldn't be difficult.
The reason there are no clones is that Atmel don't document their debug protocols though a lot of it has been reverse engineered.
awneil I thought that the EDBG chip was just an ordinary Atmel MCU
Yes, it is - just like the ST-Link is just an ordinary STM32
If that is the case then cloning it shouldn't be difficult.
Yes - that was my point in #6
The reason there are no clones is that Atmel don't document their debug protocols
But neither do ST - do they?
clawson But neither do ST - do they?
Except that the code inside it is presumably "secure" (or at least as secure as the lockbits though I think there are some models of AVr32 that have a "vault" which is presumably something quite a lot more secure).
I don't think that will stop anyone... Last time I looked they were doing simple things like placing a metal plate over the lock bits to prevent erasure with UV, which is easily circumvented by holding the UV light at an angle so it bounces under it.
