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This http://www.allaboutcircuits.com/projects/update-the-firmware-in-your-esp8266-wi-fi-module/ is a simple and easy guide to update the AT firmware on an ESP8266 WiFi Module. I've sucessfully used this method to update firmware on an ESP-03. If trying to upload Lua Firmware, please use the Node MCU flasher/updater instead.
esptool.py can also be used for more advanced firmware flashing (and also flashing from a Raspberry Pi).