I also lament the loss of the slick calibre/iPad/Marvin sync capability.
I use "home" and "away" manual approaches to get books into Marvin.
Home: I connect my iPad to my PC and use iTunes File Sharing to add books directly from my calibre library to Marvin.
Away: Because I'm neurotic about a major catastrophe wiping out my calibre library, I keep a copy of my entire library in a cloud service (I use BOX). It is very easy to use Marvin's "Get books" and "Picker" tools to download directly from BOX.
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