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I'm working with the Pi CM3+, which has 32GB of flash memory (at least my specific one does). While of course it needed an image on an SD card to initially boot, since then it has been operating solely off flash. Having configured everything and set up a bunch of programs the way I want them, I now want to create copies of the system to make multiple Pis with these settings and files. However, every search result I get assumes that the user is working with an SD card that can simply be plugged into a Windows machine, not onboard flash. Can I clone the flash to an SD card on the Pi itself? OS is Raspbian Lite, so no GUI.

Edit: Upon further research, the flash on the CM3+ uses the same pins as the SD card reader on the interface board, meaning both cannot be used simultaneously. I'm currently trying @Milliways' suggestion below

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