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In EndNote, go to Edit, Preferences (on a MAC, go to Preferences), then select "PDF handling." You may choose to rename your PDF and you can choose a folder on your computer (including Dropbox) where you house PDFs and have them copied to your EndNote library. If you select "enable automatic importing," each time you add a PDF to the selected folder, it will be copied to your EndNote library. EndNote does this through the DOI, so any PDF without a DOI will copy the pdf only, without any part of the reference added.