Update flashing instructions in README.markdown.

README.markdown

@@ -11,7 +11,9 @@ This is the documentation for the DStat microcontroller firmware.
 	* [Fuse bits](#fuse-bits)
 	* [Firmware files](#firmware-files)
 		* [Using Make](#using-make)
+		* [Using avrdude directly](#using-avrdude-directly)
 		* [Atmel Studio 6](#atmel-studio-6)
+		* [USB DFU Flashing (experimental)](#usb-dfu-flashing-experimental)
 * [Connection and testing](#connection-and-testing)
     * [Mac OS X and Linux](#mac-os-x-and-linux)
 	* [Windows](#windows)
@@ -84,12 +86,13 @@ This can be done from the [Fuses](http://www.atmel.com/webdoc/atmelstudio/atmels
 ## Firmware files
 The memory files used to program the microcontroller are found in the root directory:
 * Firmware: `dstat-firmware.elf`
+* Bootloader: `atxmega256a3u_104.hex` (See note below)
 
 Before programming, make sure your programmer is connected to your computer and its PDI connector is connected to the pin header labelled AVR-PDI on the DStat.
 The side with the red wire should face the pin labelled 1 on the PCB.
 
 ### Using Make
-Similar to building from source, the make command can be used to program the microcontroller.
+Similar to building from source, the make command can be used to program the microcontroller using avrdude (which must be present on your system).
 By default, the Makefiles are configured to use an AVR ISP mk2 connected over USB.
 If you are using a different programmer, be sure to set the `AVRDUDE_PROG` and `AVRDUDE_PORT` options in the `config.mk` files found in the DSTAT and EEPROM init directories.
 See `man avrdude` for more information about these options.
@@ -98,9 +101,14 @@ To upload the firmware file and set fuse bits:
 ````
 	make program
 ````
-Occasionally, setting the fuse bits may fail.
-If an error occurs on verification, simply run `make program` again.
+The first time the fuse bits are set, verification will fail—simply run the command again.
 
+### Using avrdude directly
+The make command simply invokes avrdude.
+Avrdude can be used directly if preferred (changing the -P and -c options to reflect the programmer you are using):
+````
+    avrdude -p x256a3u -c avrispmkII -P usb -U flash:w:atxmega256a3u_104.hex:i -U application:w:dstat-firmware.elf:e -U fuse4:w:0xff:m -U fuse2:w:0xbf:m
+````
 
 ### Atmel Studio 6
 Follow the directions [here](http://www.atmel.com/webdoc/atmelstudio/atmelstudio.AVRStudio.ProgrammingDialog.Introduction.html) to program the microcontroller.
@@ -108,6 +116,25 @@ Be sure to select `ATXMEGA256A3U` as the Device and `PDI` as Interface.
 
 In the Memories tab, `dstat-firmware.elf` should be selected for Flash
 
+### USB DFU Flashing (experimental)
+Version 1.2.3 PCBs are equipped with a switch that can be used to put the DStat into a USB flashing mode.
+If the switch (SW1) is depressed while plugging the USB cable in, the DStat should boot to the DFU firmware (if done correctly, no LEDs should be lit on the board).
+In this mode, the firmware can be updated over USB using Atmel FLIP or avrdude.
+
+Using make:
+````
+    make dfu
+````
+
+Using avrdude directly:
+````
+    avrdude -p x256a3u -c flip2 -U application:w:dstat-firmware.elf:e
+````
+
+Note, DFU flashing will only work if the DFU bootloader is installed and can't be used to set flash bits or flash a new bootloader.
+Unfortunately the XMega doesn't come with a bootloader installed, so flashing with a PDI programmer must be done for at least the first time.
+
+
 # Connection and testing
 If the firmware has been successfully applied, it will be possible to connect to the DStat over USB.