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I don't know of an ebook-manager application as such. Calibre has a CLI interface for individual tasks. If you're a CLI guy no doubt you're comfortable with scripting? I have written a couple of scripts that manipulate the calibre library using the calibredb command. You could easily create scripts to do all the management that way.
That said, if you were to use Calibre as your 'engine' then you are tied into using its database and folder structure. The later in particular is an issue for some folks.
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