Aleh Cherp on trying out the Papers 3 beta:
All documents are stored together with meta-information in a bundle not accessible to other software.
Aleh did receive some clairifiaction from the developer:
If the Dropbox synchronization is not switched on there is still a possibility to control naming and storage of files, much like in Papers 2. However, the files are still kept in a bundle not accessible to Spotlight. The support staff says that Spotlight index will be added in future versions.
I am with Aleh Cherp over at Academic Workflows on Mac. I would really like to have both Dropbox sync and easily accessable/readable file structures for my PDFs in my reference software.
I know sync is not easy, but I am really looking for a great reference, storage and cite software that works across Mac OS, iOS and even windows seamlessly. I have used Zotero as well for a long time, but it support on iOS is still painful and not user friendly.
Ok, if you just do the first two great, you do not have to worry about windows. ↩