First of all i have to excuse myself... i'm not very used to mailing 
lists and i'm also not in the mailinglist of your project.

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 > aupd.fw is probably the /bin, /usr/bin where all the softwares lies.
No, it's the firmware update for the FlashROM.

 > And then, I "guessed" that aupd is the software because I suspect 
aupd to be a shortend for "AUdio iPoD [software]" (all the audio part of 
the ipod).
Duh... please read here: http://www.ipodlinux.org/Firmware

 > Surprisingly, you can modify it at will, the iPod will boot anyway.
Not 100% true. A complete new firmware (never used, including osos aupd 
and rsrc) differs from a already used one. The id (32-bit) of the aupd 
image is set to zero. If you then restart your iPod it will perform the 
Flash ROM update and then change the id to 1 (which means that the iPod 
is decrypting aupd and then flashing it to the Flash ROM). So if you 
chage the content BEFORE updating the Flash ROM you might have luck and 
the iPod complaines about a not valid aupd image or in a... well, not so 
good case it will happily update the Flash ROM and you have a new paper 
weight because you've "destroyed" B&W DiskMode, DiagnosticMode and the 
bootloader.

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