I have been having a lot of fun upgrading my toolset for building AVR applications and hardware solutions. I have been playing around with both the raw WinAVR toolset as well as AVR Studio from Atmel. I also recently obtained a JTAGICE mkII from Atmel to hopefully be able to do some realtime debugging on my projects rather than having to always put serial port print statements in for debugging purposes.
The ATMega328 does not have a JTAG interface but instead has a one-wire On Chip Debug interface called debugWire. I do all my programming of the chip using an ISP (In System Programming) interface.
The Atmel device implements the notion of "fuses" that are basically switches that control certain feature or modes of the device. One of these fuses (DWEN - debug wire enable) is used to enable/disable debug wire mode. The debugWire pin is shared with the reset pin, so automatic reset hardware has to be disconnected for debugWire to work, which according to the Arduino Uno schematic is a non-issue.
So, for debugging you start in ISP mode to set the DWEN fuse. Unlike JTAG chips which have the JTAGEN fuse enabled by default the debugWire chips have DWEN disabled by default.
Once you have used ISP to switch to debugWire mode in theory you only need two of the 6 wires in the ISP header but as you need all 6 to get the chip back from debugWire to ISP mode (you can't change fuses in debugWire mode) you might as well leave all 6 connected. While in debugWire mode, the ISP mode is completely disabled.
So, since Murphy is still on the payroll of course, my first debugging experience ended up putting my ATMega328 in a mode where it can no longer debug, but the ISP interface is disabled so I can do nothing with it.
One possibility is that I have messed up the system clock fuses somehow. If that is the case, I should be able to apply an external clock to the chip and get it back. The other option is to use high voltage programming which should be able to recover from any of these states and get the fuses back to a coherent state.
So, my next project will be to build a high voltage programming setup. Oh sigh... Probably just as well as I need to build one of these HVSP (High Voltage Serial Programming) jigs eventually anyway...