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Also; try to think of calibre as a black box; the fact it happens to store eBooks in files that you can access manually should be thought of as irrelevant. Kovid could always have selected obfuscated file names, and directory names, or even have implemented an encryption scheme on the files themselves.
For what its worth you could keep a single copy of the files OUTSIDE of calibre, and then allow calibre to manage another set for it's own purposes.
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