rusefi.bin file is compiled rusEFI firmware. Sometimes you would have
rusefi_no_asserts.bin variation of this file with fewer safety checks.
rusefi.dfu is also compiled rusEFI firmware, that file is used for DFU mode of flashing.
rusefi.ini is TunerStudio project template file, you would use it if you use TunerStudio software to tune your rusEFI unit.