Update on file organization in Papers 3

Here are some clarifications concerning handling of documents in the beta version of Papers 3 which I criticize in the previous entry. Responding to my query, Papers 3  staff confirmed that switching on the Dropbox synchronization (a new feature in Papers 3) removes user control over how the documents are named and stored. They added:

We are looking into a way how we could re-introduce the file organization with Dropbox syncing but we can’t guarantee if/when it would be available.

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.

Moreover, if you switch on Dropbox synchronization once you won’t be able to restore control over organizing your files even if you later switch the synch back off and move your library to a local folder. This behavior is  unexpected and I hope it can be corrected in the future. Otherwise an accidental click on a button in the Preferences may cost people their whole libraries!


About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He researchers energy and environment and coordinates MESPOM, a Masters course operated by six Universities.
This entry was posted in Bibliographies and tagged . Bookmark the permalink.

10 Responses to Update on file organization in Papers 3

  1. Dellu says:

    It is frustrating when your files are not accessible from other apps and Finder. I have struggled with the same problem using Sente; and finally came up with a solution:
    I have written it here –>http://dellu.wordpress.com/2013/01/10/sente-and-dropbox/
    syncing local bundles into Dropbox effectively; makes the bundle available to spotlight too.


  2. Dellu says:

    Even easier method would be to use this little app called MacDropAny which can automatically create symbolic links for you.


  3. Carin says:

    I´m very glad I found you two last entries on Papers3. I will definitely wait to upgrade and start looking around for other options if naming and storing files is not the same as in Papers2, or one can find a good, reliable work around.


  4. That solves the mystery. Has anyone played with Sente lately? I know there was a big update recently. Dellu, thanks for sharing that work around. I will check it out.


    • smrs says:

      Sente is great in every way, except when it comes time to add cites to your manuscript. Then it is clunky and awful, and cites still can’t be added/scanned with “track changes” turned on. Big problem.


  5. Martin Boycott-Brown says:

    This is very bad news. It makes Papers 3 unusable for me. I will definitely not be upgrading. I would never make annotations or notes inside my bibliographic database manager. I need everything to be portable, not “trapped” inside a program. I usually use Skim for annotations and Devonthink for notes, and try to use plain text as much as possible. I sometimes use PDFPen or Devonthink to OCR a pdf. Papers 3 would make everything more difficult.


  6. Francis says:

    I have the Dropbox option activated (the folder was moved to the dropbox folder) but the files are still organized in folders by year and author. e.g.: ~/dropbox/library.papers3/Unknown/articles/2013/author). if I use Spotlight, I can search for particular authors as well.

    This has been working under Mountain Lion and know Mavericks using Papers 3 beta 7a


  7. emzed2 says:

    Hi — Matias (@mz2) from Papers here. We have now solved the file organisation problem in a Dropbox syncing compatible form for Papers 3.0 announced just yesterday.
    The new way of organising files is safer in the context of syncing (the older method of moving actual files on disk that is Dropbox synced could not be given guarantees for) but also quite a lot more powerful than what was available in Papers 2 and earlier: for instance you can browse to the files using many of the the same criteria as in the main app itself. It’s also very flexible for future extensions, so stay tuned for more file organisation features 🙂


    • Ben K says:

      Hi, thank you for your email. I am considering moving from EndNote to Papers and the ability to search my files from spotlight and access them from other applications, as well as have control over the naming convention regardless of how they are sync’d/backed up is very important to me. Just to make sure I understand correctly, is this functionality up and running in Paper 3 at this time? Thank you very much.


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