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I am the lucky owner of a Rev A jtagicemkII. I was unable to program the boot
section of a xmega256a3b with the listed patches (rev3 + ..private.h mods),
using the JTAG protocol. Main flash section and fuses would program OK. With
AvrStudio5 my mkII would program the boot section of the chip, so I could not
leave it to that!
After experimentation I found that setting the offset to zero vs 0x84000 did
the trick. (only for boot section programming)
I have made a quick fix and included rev3 patch modifications plus missing
xmega_boot_jtag.patch to be used against avrdude-5.10