Can I remove the 2 headless start files which are located in /boot? Specifically, can I remove ssh and wpa_supplicant.conf after I've finished the first boot and reconfigured everything with raspi-config?

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I am assuming you are talking about Raspbian. At the first boot from a newly prepared SD card, if an ssh file and a wpa_supplicant.conf file are found in /boot then they are both moved. You would not be able to delete them, as they would be gone already. If this does not happen, something is wrong.

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