I have been using a Kindle Keyboard which does support audio which is why I mentioned the audible and music directories. I didn't even notice that the new Kindle 4 I got for my wife doesn't support audio.
The system folder on the new Kindle 4 contains the following two directories:
"Search Indexes"
"com.amazon.ebook.booklet.reader"
both directories appear to contain stored application data or preferences. Not sure either is required for your Kindle to function properly.
The active-content directory is probably used to store Kindle apps and/or associated data.
My Mac is showing the Kindle 4 has a 1.46GB drive, 1.4GB available, with 55.1MB in use.
If your Kindle is functioning properly then it doesn't seem like you should be too worried about the missing system folder.
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