Quote:
I would like to write notes about various Bible texts in the format "Jn 3:16" for example and be able to cross-reference between other verses mentioned in the notes themselves.
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What would be wrong with using a text editor plus a terminal in which you bible(1) (the package is called bible-kjv on ubuntu, fwiw)? You can write notes in the text editor. You can access the referenced verses readily. Using the editor's search function, you can see where you also refer to the same verse.
What do you want to do that this doesn't do?
[...] Have been unable to find a stand-alone note-taking solution that works here.[/quote]
What software have you tried? Have you tried gnomesword2? What does the software you have tried do? How is that different from what you want?