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We don't do cut-and-paste from the PDFs. With the exception of the first few books we did, everything is processed using a bunch of heavily automated tools. These tools include dictionary searches to fixup the vast majority of the traditional problems with pulling text out of PDFs, such as the common issues with ligatures you cited. We probably catch and fixup over 99% of the issues. Unfortunately, the tools aren't perfect and the dictionary doesn't know about adventure-specific terms like "flayleaf", so they didn't catch and fix that one. But they definitely caught all of the references to "halfling", I'm guessing. That one obviously didn't get caught during the proofing pass, either.
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