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Right, PaperCrop turns it into an image-based PDF, but soPdf should keep it however it was to start, so text-based to text-based, so your dictionary should still work. (It does lose bookmarks and internal links, however, unfortunately.)
Calibre comes with a command-line tool called pdfmanipulate, which can be used to crop. I don't have any experience with it, personally, however.
There's also the pdfcrop tool from the LaTeX bundle, which works fine for me too.
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