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On the Pepper Pad 3, the MobiPocket Reader stores all the ebooks it "knows" about in a single directory. However, it has an "import" option (in this case import from USB) that can navigate subdirectories. An imported file is copied to the mobipocket reader directory.
In a sense FBReader works the same way for .mobi books (which are not automatically imported). Its "add book" option can navigate the full file system, but once the book is in the library navigation is via author (and series) and title. However, FBReader does not make a copy of the imported file - it is left in place.
Under Linux, softlinks can be used to both leave files in place and have them in a particular directory. However, robustness suffers (softlink may point to a missing file).
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