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Skrib also seems to lose the navigational data from *Office.
So it looks like my options include:
1. Continuing with NeoOffice, no change.
2. Splitting files in NeoOffice, organizing in Calibre, and writing in NeoOffice.
3. Splitting files in NeoOffice, organizing in Scrivener, and writing in Scrivener.
4. Splitting files in NeoOffice, organizing in Dokuwiki, and writing in DokuWiki, since apparently it has better footnote support than most personal wikis. It requires a special plugin with its own dependencies to import and convert.
I'd initially dismissed #2, but it's looking more appealing.
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