I'm not sure if this answers your question or not, but you can easily put music on the iPod via iTunes without it ever touching the iTunes database. Start up iTunes and plug in your iPod. The iPod will show up on the left-hand column. Click on it to show what's on the iPod. Now just drag stuff from your filesystem into there. It will just put it on the iPod without iTunes ever trying to do anything with its database at all. That doesn't provide any way for automatic updates, but I don't know if that's something that the iTunes/iPod combo would do nowadays anyway, or if you'd be interested even if it did.
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Bitt Faulk