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I have read first time about JTAG. If I understand it right it is only to test everything.
http://de.wikipedia.org/wiki/Joint_Test_Action_Group (German)
here is a interesting discussion with one known person involved :-)
http://www.xcore.com/forum/viewtopic.php?f=44&t=2477
The original purpose of JTAG was to allow board manufacturers the ability to test assembled boards with a minimal hardware interface. By chainging them serially and setting a common interface spec even dissimilar chips can be polled and verified in a single JTAG loop.
As used with XMOS chips like Xena, which usually keep the executable code in RAM, it allows that ram to be programmed, and also allows setting of various configuration options such as links between cores(tiles), PLL clock divider settings, and other various details required to get a XS1-L16A chip up and running.
Within the realm of hobbyists, the XMOS chips are almost exclusively run this way, since the OTP ROM is, well.. One Time programmable. It'as not flash, and once it has been progframmed, that chip is committed to that code forever.
Obviously Flash would be more hobbyist-friendly, but it would also create security concerns for any commercial products made with XMOS chips.
Getting back towards the topic(s)..
The non-Amiga XMOS hobbyists are largely oblivious to all these JTAG details. The XDK suite provided by XMOS will seek out XMOS compatible JTAG programmers on startup, then access those to get ChipID's, and often board IDs from the JTAG device. Net result, it's all super-automatic, hands-off, and self managed. Just plug your stuff in and everything is configured automatically. All of this is wonderfully convenient, but it leaves those with non-XMOS kit out in the cold, so to speak.
The discussion you referenced is about one of the "new" products from XMOS. They are now building the USBtoJTAG directly into their newer kit, and doing it in a way that can NOT be easily reached from an external JTAG programmer. This means that we will not be able to use these new "StartKits" from an X-Series AmigaOne, because there's no place to connect JTAG to it.
They are meant to be used only on XMOS supported platforms with XMOS authored software.
Eventually a few hackers found a way to (somewhat) get around this, but not without some loss of function.
Veering back towards a topic once more.. JTAG on Xena is required to load any Xena program you wish to run, The JTAG loop is extended to the XORRO board, so that additional XMOS chips can be added at will. The XMOS tools that we have can load code into any number of XMOS chips through this loop, as well as freeze execution and read the current state of all the chips in the JTAG loop. This can be useful for debugging. We can dump RAM, registers, switch states, ROM, lots of stuff I have not yet documented. There is also a XReset command that will drop all connected (or any one connected) chip back into it's inert power-on state. While these are technically command-line tools, they work with tooltypes as well. Any XMOS program that sets XRunXE as it's default tool with load up when double-clicked.
About adding DB connectors to the Xorro board, that is possible, but I would discourage it. Perhaps I am overly cautious, but anything I connect that comes outside of the case will be optically isolated. While this may be overkill, I think it a prudent choice. I have an SD card there now, no need for isolation. I have a MAX3232 chip, which is connected to the serial port inside the case. again, no need for isolation there. But anything that comes outside the case, for joysticks or whatever else, will be isolated on my machine, and I would suggest that others consider it as well.
Intersting thought.. the S/PDIF in and out connections are optical by design, so adding those should be as safe as anyone could hope.. a very easy way to get high bandwidth audio in and out of the Xena chip.
I am being called away..
LyleHaze