[btrettel]

I use Zotero for references but keep the files in a separate organized directory structure, where the filenames match the citation key in Zotero. Each approach has its own advantages and disadvantages.

The largest advantage of the directories is speed. I don't need to wait for Zotero to launch, and Zotero has gotten much clunkier over the years. (I think they need to do an entire rewrite at this point.) I also have some bash aliases to, for example, open a PDF file I have in my reference folder given only the citation key.

Zotero is better for annotations, and other information associated with a citation. I make very heavy use of the related documents pane. I also often put citations in multiple folders in Zotero. That's a bit more complicated in the directories as I need to add links and then maintain the links. (I have a few shell scripts to help with the creation and maintenance of the links.)

Zotero also makes generating bibliographies in different formats easy. I normally use BibLaTeX format, but a journal I'm submitting some things to requires BibTeX. The conversion was dead simple in Zotero. If you manually curate your bibliography file then this would be a pain.

Also, I have many citations in Zotero where I don't have a copy of the document. Not all documents have DOIs, and not all documents have been digitized. I use Zotero extensively when visiting the library so I can keep track of which documents to scan.

[SebiH]

> I use Zotero for references but keep the files in a separate organized directory structure, where the filenames match the citation key in Zotero. Each approach has its own advantages and disadvantages.

Why not install the Zotfile plugin [1]? You can configure it to do exactly that, and point it to a Dropbox folder to get better synchronisation between devices.

[1]: http://zotfile.com/

[btrettel]

I wasn't aware of Zotfile. I'll take a look. Thanks. Hopefully it has some way to automatically associate with ~10,000 files...