Papers lets you organise your documents on your disk the way you want. Whether you want your documents organized in subdirectories by journal, by author last name, or a hierarchical combination of year and, Papers manages all the documents in your library automatically.
Select the "Library" tab:
By default, the library is stored at Application Support/Papers2 . You can change the location of the Papers Library Folders at any time. Simply click on change to choose the destination for your library.
Papers doesn't just organize your files, you can also select whether you would like to keep the original copy of your file on your hard drive, or if you want Papers to delete it once it is imported into your Papers Library. For this to be possible, the box beside "Copy files to Papers Library folder upon import" has to be checked first.
You have complete control over how Papers organizes your library
of files into subdirectories. You also control whether Papers uses
subdirectories. By default the papers are organised in
subdirectories in a three-level hierarchy, based on category, year
and author name. If you do not wish to use subdirectories at all,
just uncheck the box:
If you do want to use subdirectories, you specify by what parameters Papers should organize your library. Papers can create directories based on category, author, source, editor, and publisher. You can build your subdirectories based on any number of combinations of these, in whichever way makes most sense to you.
For example: You may want to organize your documents first by author, then by category, and then by source. Keep in mind that each article will now be allocated to a folder based on the source of the article, a collected of source folders are within a category folder inside a folder dedicated to one particular author.
One of the most powerful features of your Papers Library is its automated document renaming functionality. Finally the days of manually renaming documents are over, as are the days of sorting through hundreds of documents named "sdarticle10012993.pdf". By default, the source (e.g. journal name), year and author are included in the document name, to produce file names such as "Nature_Watson_1953.pdf". Same as the library location and folder structure, the document naming pattern can be adjusted in the Library Preferences tab.
You can completely personalize how you would like Papers to rename your files once they are imported. The way in which you choose your documents to be renamed depends on your personal preferences and how you use your library. For example, you may want each file name to start with the author's name if you work in research and spend quite a bit of time citing other papers. On the other hand, perhaps starting each file name with a category term or source will help you organize your files if your library is build around different business projects.
There is always the option for Papers not to rename your files. If you prefer to keep your files named as they are (for instance if you are a lawyer and your secretary assigns file names based on case numbers or other parameters that are important to you). Simply uncheck the box next to "Rename files in library folder as".