BibDesk2Zotero (with attachments) is a pair of files that should allow you to convert a BibDesk bibliography (in BibTeX format) containing local file attachments in the form of (Bdsk-File) to a new BibTeX file that Zotero can import along with all of its attachments, using the (included) BibTex.js translator file. All attachments (excepting entire directories) in each entry present in the original BibDesk file should come along seamlessly into Zotero.

Important: To convert successfully, the BibDesk bibliography file must be in the same directory as the attachment root directory. (i.e., if you have a "Papers" directory containing PDFs, movies, etc., the BibDesk file must be located in that "Papers" directory. You can move or copy it there if it's not already, of course.)

BibDesk stores attachments as Base64-encoded pathnames. Currently these are ignored when importing a BibTeX file into Zotero. To enable import into Zotero, these entries must be decoded to actual filenames and given a new field that the appropriate translator can recognize.

• run the command perl bdsk-to-zotero-attachments.pl /PATH/TO/OLD.bib /PATH/TO/NEW.bib to create the new, attachment-import-enabled BibTeX file.
• install Zotero Better BibTex (as per this issue, Zotero Better BibTex supports the Local-Zo-Url-N "out of the box").
• Quit Zotero standalone
• Then launch Zotero standalone and perform an import of NEW.bib

• Scans your BibDesk bibliography for every instance of "Bdsk-File-N", which indicate local attachments.
• Decodes the Base64-encoded pathname of the files
• Writes out a new BibTeX file with the correct pathnames, listing each under a new field "Local-Zo-Url-N"

• Last tested on MacOS 10.12.4, Zotero Standalone 4.0.29.15, BibDesk 1.6.11, and Zotero Better Bibtex 1.6.97. As of 2017-05-15, this still works.
• Requires system utilities "dirname", "grep", "tail", "base64" and "plutil" (standard on Mac OS X).
• Requires that the directory /tmp exists and is user-writable (can be customized).
• Correct functioning of the program depends on the current way that BibDesk (as of version 1.5.10) encodes local attachments, and on the way that the Mac OS X "plutil" prints out the XML. Any changes in these factors will produce unexpected behavior.
• Does not recursively import entire directories as attachments, but prints a warning to STDOUT that the directory was ignored.
• As stated at the top, the BibDesk bibliography file must be in the same directory as the attachment root directory. (i.e., if you have a "Papers" directory containing PDFs, movies, etc., the BibDesk file must be located in that "Papers" directory.)