I think I'm getting a little closer to the source of the problem.
Here is a quote from the README file from the github website
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Quote:
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- Do your editing (saving changes to a local temporary epub somewhere if you must). Remember to use "Mend and Prettify" after you're done, and always make sure the epub validates with no errors. Then when ready, save the contents back to the "src" directory of your local, cloned repository using the [FolderOut Sigil plugin](https://www.mobileread.com/forums/sh...d.php?t=293649).
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In my first two attempts, I had taken the suggestion 'saving changes to a local temporary epub somewhere if you must' in the order in which it was written.
For this 3rd attempt, using a fresh clone, I ignored that save, ignored the prettify (because my edits respected the original layouts) and went straight for the F7, Epubcheck, FolderOut.
Results in the screenshots attached.
You see only 3 files changed (+ the content.opf file).
So it looks as though it was the action of saving myself a temp.epub before the FolderOut action which caused the unwanted stuff. Does that sound reasonable?