This is a little utility for rewriting a BibDesk BibTeX file so that it can be read by Zotero with the file references intact. BibDesk and Zotero mostly get along except for the way BibFile stores links to documents like PDFs. This utility Base64 decodes all Bdesk-File paths, parses the serialized plist, extracts the relative path to the file and adds it back to the bibliographic entry as an absolute path.

pip install bibdesk2zotero 

$ bibdesk2zotero citations.bib /path/to/pdf/files/ > new-citations.bib