The epub3 spec is unclear. All throughout the spec they talk as if the navdoc is a required separate xhtml file. No where I could find in the epub 3.01 spec did it say that it could be mixed into a more general xhtml file. That said, I could not find a clear line that the navdoc MUST be the only thing in that file either.
Given the navdoc is machine parsed by reading systems (but still usable for human viewing) I think it would be safest in its own doc with the nav property set in the manifest.
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