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I think the Calibre plugin is just fine, and quite easy to use. Since you're already IN Calibre to manage your collection, I think it makes the most sense to use the plugin there. It quickly becomes part of your normal workflow.
If you're starting with some collections already, just import them the first time, and then use the Create option from that point onward. You'll need a custom column to keep collections information in. Mine is labelled "Collections". (Duh.) And Calibre will give you a drop down list for which collection(s) to put each book in.
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