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Xournal is just a reader/note taker and a means to annotate pdfs in a relatively straightforward manner. It is an application.
I've never used the DR1000's inbuilt notes function as Xournal is a lot more useful for me.
There is no replacement for the Companion software, not that it served much use anyway.
I'd upgrade to the last version of the DR firmware unless you need the mobipocket reading ability. Version 3 moved to epub and is a much nicer experience. Most applications have been moved over to expect the latest firmware.
regards, Howard
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