Moving from Bibdesk with many, many PDFs

Hi,

thanks for using JabRef!

There are multiple possible solutions:

  1. In the settings you should configure a file directory pattern with the value [bibtexkey] and your file name pattern according similar
    And you should tick the check mark “Bibtex file as main file directory”

A File directory pattern will move your file to subfolders according to the specific pattern (e.g. if you use entrytype, all files would be grouped by type: e,g. article, incollection etc)

Associate pdfs: I think the correct one is here “Automatically set File links”

2.) Regarding the pattern: Have you checked the help page ? You can customize your bibtexkey:
http://help.jabref.org/en/BibtexKeyPatterns

Renaming of Files : Quality -> Cleanup -> Rename PDFs

Regards
Christoph