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I have an SD card that I want to copy the firmware / memory from, my question is what pinouts do I connect to the SPI programmer and what are the commands to copy all of the firmware /memory. Thank you.

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The SD card controllers are usually embedded deeply into the card and do not offer easy access to their firmware (SPI or otherwise). However, they may have undocumented backdoor commands over the SD interface that are used for factory testing.

You can find the details and investigation of one family of controllers in bunnie & xobs's 30C3 talk: slides, video, code, blog post

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