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I am looking for a way to assign tags to existing .pdf's (or other ebook files formats) without having to modify/move/copy any of them, on Windows. This is due to me already having them in an organized folder structure that I like.

How do I manage my eBooks files and add tags to them?

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Your most recent edit changes the question entirely. Are you looking for a way to add tags to .pdf's in general, OR how to add tags to .pdf's using Calibre? There's a big difference here. –  KronoS Jun 19 '13 at 20:23
    
Since you haven't responded back to me I've reverted the question back to my edit to keep answers relevant to that. If you're looking for something different (i.e. how to use calibre to tag .pdf's) then I suggest a rework of this question or even better, asking another question related to that. –  KronoS Jun 24 '13 at 16:01
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For PDF's I recently discovered Mendeley. It's cross platform (currently using it on Windows and Ubuntu), and also offers a few gigabytes of free online storage for syncing books, if you want that feature. It has tagging and folder functionalities, tabbed interface, annotation tools, and remembers where you last left reading. Personally, I don't like the interface of Calibre and the fact that I found it to be quite slow.

However, it doesn't support ebook formats (e.g. epub), which is a shame since it is a really good free software. I recommend you still have a look at it though, like I did when I needed something to read books on and wasn't disappointed!

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Although your question asks how to tag e-books without moving them around in Calibre, I've had the same problem and couldn't find a way to do that using Calibre. (Perhaps your question should be 'What ebook reader allows me to tag my book without copying/moving them?')

Instead of Calibre, I use FBReader, which doesn't move your files and does allow tagging. It's available for GNU/Linux, Android, BlackBerry, OS X and Windows.

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