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BTW, JTAG ICE HW capability is there but the firmware is quite limited since Atmel dropped the support many years ago. I think there are quite some people who want to improve the FW to support more functionalities. However, I have not seen something concrete. The clones of JTAG ICE are really cheap (quality varies) and it is easy to DIY as well, unlike the clones for JTAG ICE mkII which are still quite expensive (that is why I have no interntions to get it).
Atmel also dropped the support of JTAGICE mkII later (not so sure when).
The latest Device supports only lists Atmel-ICE/Power Debugger and later. But the drop-down menu of latest MPLABX IDE for ATmega406 still shows JTAGICE3. https://packs.download.microchip.com/DeviceDoc/Device_Support.pdf (for PIC/AVR/SAM, some tools are PIC only)
... but on the ATmega406 it's bit 1
And here an example where it is used:
avrdude/src/jtagmkII.c
Lines 98 to 107 in d6c61f5
avrdude/src/jtagmkII.c
Lines 1350 to 1352 in d6c61f5
Not a biggie (false alerts) but should be fixed at some point.
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