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Why not use one of the command line suggestions from the previous thread; you would have to change the extensions on the input and output files from mobi and epub to whatever you desire.
There would be no crud; no extra directories; just a file with a different extension in the same location as the original.
I hate to say though that the reluctance to try to fully use a tool is a real shame. Yes; some of your loving configuration and happiness will be lost, but, try to seriously work with the tools.
After adding material, take the time to ensure that the datum for it is correct before rushing headstrong to conversion; take time to loving massage the author and title fields, maybe even the series info.
Only when the initial work is done start on the conversion exercise.
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