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@Gregg Bell - I suggest you try the one in the calibre-editor first, for a start it does the unravelling of the ePubs for you etc. I've used it a few times when I've gotten myself confused with what I've already done and not done, right and wrong.
The editor can be used independently of the library manager, I have it as one of the file associations for .epubs, same as I have for Sigil, etc.
I have a recollection Kovid said he created the calibre editor's file compare tool from the tool he uses in his daily work, so a) it's tried and tested and b) having it in his toolkit made it relatively easy to fold into the editor.
BR
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