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One trick I like to do in my libraries is to use a custom hierarchical field to store a pseudo directory structure in Calibre. It requires a little work to populate the field, but once you do, you can use the tag browser as something like the Folders pane of Windows Explorer.
This addressed most of my complaints about not being able to look up the files the way I wanted when I first started using Calibre. You still do all your work within Calibre, but at least you have a nice, familiar hierarchical structure to work with. It also makes save-to-disk templates easier.
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