Papers 3 have just graduated from the beta version! Here is a couple of first quick impressions. There is a change in handling of files, which many people intensely discuss here and which is a make-or-break feature for a pdf manager. In the beta versions of Papers 3 the files in the library were virtually not accessible. Papers 3 Preferences now assure the user that the files in the library are accessible through Finder:
This is exciting, but a bit of an exaggeration. What you see in Finder are aliases, not files. They are nicely organized not only by Authors, but also by Keywords, Collections, Sources, etc. However, you can’t tag them (aliases are not taggable in OS X). Good news: if you tag the original files (e.g. before importing them into Papers), the tags will also be assigned to aliases. Bad news: Spotlight does not seem to recognize or index these files/tags. It was possible to index the virtual disk in DevonThink, but it was extremely slow and the tags still did not show up for me.
Another slightly irritating feature of the Beta versions was the inability to merge duplicate entries. Now it is possible. First, select the duplicate entries you want to merge (to see all duplicate entries in the Library go to View – Show Duplicates). Then select Merge Duplicates from the Papers menu (or from the right-hand inspector at the bottom of the screen). Review the data for the merged entry and confirm the merge.