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To be honest, I can not imagine of JTAG to be the option for in real world operating systems - but anyone can correct me on this..
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I don't think that JTAG is used as the only configuration option once in production either, but you should still think about putting a JTAG connection on the board anyway. First it can be used for debugging (and even after production, you can always need to debug something at any time) and during board manufacturing the connector can be used for boundary scan.
So put a JTAG connector, in combination with PS or AS as explained by Carlhermann.
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