But help is in sight! I added a plugin to KRename, which can rename files based on meta-data included in PDF files. Organising a large set of publications is now a matter of adding the PDF files to KRename and using the template "[pdfAuthor] - [pdfTitle]". Convenient, isn't it? The screenshot below shows KRename while renaming a few PDF files.
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The supported tags are [pdfPages] (number of pages), [pdfProducer], [pdfTitle], [pdfSubject], [pdfKeyword], [pdfCreator] and, [pdfAuthor]. If you have an idea for further meta-tags, do not hesitate to contact me. It should be quite easy to add more information, the current implementation is a matter of 10 lines thanks to the PoDoFo library used.
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A pity is that many PDF authors do not add proper meta-data to their PDF files. So, if you are writing on a publication at the moment, please make sure you add your information to the PDF metatags.
This feature is currently only available in KRename SVN trunk.