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Have any of you looked at Calibre? It's a free database program that allows you to edit the metadata of books (files). If these books have ISBN numbers, Calibre will pull the metadata and cover information from ISBN, Amazon, etc. and auto populate the data fields. When converting the file, either to another format or to the same format, adding the metadata to the beginning of the book is an option. PDFs are a poor format for ereaders and they don't always convert as well as other formats, so usability for you will probably depend on the quality of your files. It is very good at letting you choose a whole bunch of books and mass-edit the author, tags, etc. You can also create your own metadata fields if there are other things you want to track. There's an active Calibre forum here at MobileRead.
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