Maybe there are some plugins/add-ons that do this? I tried goofing around with Zotero a little - since it works, somewhat, with the citation style that I usually have to use, and there are a lot of great integrations for it, including Alfred - but I can't find any tools for embedding its collections as tags for the PDFs or its other metadata (e.g., authors, title, etc.). or at least one that catered to PDFs (i.e, that embedded its metadata for Finder/Alfred to use)! It'd be great if there were an all-purpose version of it. Your approach with Bibdesk reminds me somewhat of what is found in a lot of image-based organization systems, like Pixave (collections, tags, etc.). Relatedly, have you ever tinkered around with other citation managers? Frankly, since I'm not so reliant on the citation management side of things, any file organization application would work. Can BibDesk write its citation-related records to the PDF's metadata, too (e.g., author, title, etc. Then, tools like Houdah Spot could be a real tour de force (Side Note - I love the metadata window that's displayed in Houdah Spot, I wonder why they don't allow editing in this window?). This could be a game breaker! Have you done any testing with it? Frankly, for what I'd like to do, any citation management software or (file organization system, like DEVONthink) would work for me if it would embed its tags/collections/groups/whatever on the file as a tag for the native OS to view. This is doable w ith script hooks in BibDesk.
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