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I have a library of a lot of ebooks about a lot of subjects, I order them by folders, but is very common to have interesections on the topics they cover. I could tag all them with the folder name, and then manually tag the subtopics each book covers.

edit: too bad it isn't on ubuntu repositories. I've a personal policy to avoid programs outside the repositories

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Try Calibre for managing ebooks, it has a built-in tag system.

I really like Calibre, but it's tag system is pretty clunky. I don't think I can even tag multiple books at once.

It's definitely clunky, but you might like to know that you can tag more than one thing at once:

Select more than one book, right click -> Edit metadata -> Edit metadata in bulk

Not only can you have multiple tags, you can have icons which are conditionally displayed based on tags. Tags are stored in a single metadata file, one directory per ebook, so can be parsed with a script when performing bulk operations.

You can then customize search engine like recoll to display ebook metadata as contextual snippets in full-text search results. Best of both worlds.

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