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One of the reasons that I would like to have my books physically separated is my use of desktop search software. This software generally has a limited file size or number of terms. (For instance, Copernic Desktop Search is limited to 2MB file size. Yes, I have exceeded this limit.)
By limiting the software to a particular folder I can focus my searches on applicable material without exceeding the limits of the software. If you have several fields of interest and have a lot of books on each subject, keeping track of a particular bit of information is a lot easier with the use of desktop search.
Nor does it return thousands of inappropriate hits. As I maxed out Copernic, I whimsically tried a search on what I thought was an uncommon to rare word. I got back something like 100,000+ hits. Admittedly, it had searched through every website, song, pdf, text file, ebook, etc on my system.
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