I don't know if this will help any but I wrote a layman's step-by-step 
guide to updating the IOIO firmware as it took me a bit of figuring out to 
understand.

Unfortunately I am in the process of updating my website and silly me did 
not save the article anywhere;

however with a little luck google cached the page and I copied the article:


UPDATING FIRMWARE:
 
1. Open Command Prompt at folder location of IOIODUDE:
SHIFT + RIGHT CLICK -> Open Command Prompt at Folder.
 
2. Type:
"c:\Program Files (x86)\Java\jre7\bin\java" -jar "d:\Student 
Data\Downloads\IOIODude-0100\ioiodude.jar"
 
3. Download a version from the wiki and store it somewhere on the PC (I 
chose the default downloads directory)
 
4. type into cmd prompt: "c:\Program Files (x86)\Java\jre7\bin\java" -jar 
"d:\Student Data\Downloads\IOIODude-0100\ioiodude.jar" --port=COM5 versions
 
NOTE *** Instead of COM5 you use whatever port your ioiodevice is listed as 
under in your device manager.
 
5. Go to  <https://github.com/ytai/ioio/wiki/Downloads>
https://github.com/ytai/ioio/wiki/Downloads and download the latest bundle 
by clicking on the QR-Code (NOT THE DOWNLOAD LINK!) - the QR code will 
download the .app file instead of the source code!
 
6. Type into the cmd prompt: "c:\Program Files (x86)\Java\jre7\bin\java" 
-jar "d:\Student Data\Downloads\IOIODude-0100\ioiodude.jar" --port=COM5 
--reset write "d:\Student Data\Downloads\App-IOIO0400.ioioapp"
 
NOTE *** The .ioioapp file will be saved wherever you saved it upon 
downloading - adjust the above pathfile in step 6 accordingly.
 
7. Let the write happen, it should take a few seconds and a progress bar 
should appear.
 
8. You are now done! The ioio board should have the latest firmware 
installed.
 
 
EDIT: For the latest app version in 5.02 this worked:
"c:\Program Files\Java\jre7\bin\java" -jar "d:\Student 
Data\Downloads\ioiodude.jar" --port=COM4 --reset write "d:\Student 
Data\Downloads\App-IOIO0500.ioioapp"

On Monday, May 5, 2014 7:52:39 AM UTC-5, Urs Weder wrote:
>
> Hello all,
> I want to update my IOIO with the most recent firmware but nothing seems 
> to work as it should:
>
> The first problem:
> ./ioiodude --port=/dev/IOIO0 versions mostly just hangs and doesn't 
> return anything. If ioiodude returns something than it can take up to 3 
> seconds.
>
> Output (after several tries):
> IOIO Application detected.
> Hardware version: SPRK0020
> Bootloader version: IOIO0400
> Application version: IOIO0330
>
> The second problem:
> When starting in bootloader mode, the IOIO doesn't enumerate, i.e. 
> lsusbdoesn't list the connected IOIO.
>
> For these tests i used:
> Two different computers (openSuse and Win7 Prof)
> Two different IOIO OTG (both have the same versions)
> And two different cables, just to make sure.
>
>
> Greetings, Urs
>

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