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As @sfe-SparkFro has realized, the tool currently assumes for ESP32 flashes that they are formatted in the way they are released on GitHub (as a zip file with bootloader and partitions) and pulled down for non-custom firmware installs. This is not the way MicroPython itself and many other vendor releases the ESP32 firmware (usually released as standalone single .bin files) so we need to support flashing directly from a .bin.