I've recently been trying out software called "Papers". On paper, it sounds good:

Do you have dozens of PDF files from your favorite scientific articles
scattered on your harddrive? Do you also try to desperately organize
them by renaming and archiving them in folders? But like the piles of
printed articles on your desk, you can't keep up with all the new
papers you download, and despite all your efforts it has become
impossible to find that one article.
Finally that all belongs
to the past. We've been there, trust us, we know. That's why we wrote
Papers, our latest application exclusively for the Mac. Papers will
revolutionize the way you deal with scientific papers. Search for
articles using the built in search engines, retrieve and archive PDFs,
and read and study them all from within Papers, your personal library
of Science.
The problem is, it doesn't work. When you import PDFs it automatically renames and sorts the files. In theory this is exactly what's required. In practice, it cannot distinguish between different versions of the same name, and only seems to allow automatic editing. For example, I imported about 20 of Peter Boettke's papers, and now have about 20 different authors - "Peter Boettke", "PJ Boettke", "Peter J Boettke", "P Boettke", etc. This is compound by co-authored papers since the programe fails to distinguish between authors and initials. In order to correct this, you use JStor or some other scholarly search function and match the paper. But the search is time consuming and often fails to find the article. So in conclusion this promises to solve a real problem, but falls well short. Back to manual folders and filenames...
Update: an evidenctly when you drag "papers" back onto your desktop it doesn't copy the actual PDF but a text clipping of the filename. Hence I've now lost all my papers of authors beginning with A, B, and C. Sorry George, Peter and Ronald.
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