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I just took a look at the full command line documentation and I now am wondering if using your tool it might make sense to use it first on the inividual article PDF files and then use PDFtk to merge the processed files into a single PDF file. In that approach the top portion I would need to crop would be on the first page of each article. So I assume I would be able to use -cbox1 (specific figures) -m (specific figures) ./*.pdf as an argument to crop page one only and then marginalize the appropriate sections.
Dave
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