I have been using Zotero since 2006. It is one of my favourite pieces of software, and an essential part of my workflow. One of my longterm aims has been to link my PDFs to the corresponding entries in my Zotero catalogue. This sounds simple enough, but is very difficult to execute if you use Zotero on multiple operating systems because the file paths will be different. One solution is to have different PDF links for each OS. But this is cumbersome and knowing which link to click for which OS is confusing. There exist many complicated guides on the internet for syncing Zotero libraries across multiple OSes and devices, usually using Dropbox, but in most cases the steps involved are more complicated than they need to be. After 6 years, I have finally cracked it.
Here is what I use:
Firefox + Zotero*
* on my Windows work machine, and on my MacBook
^on my iPad
And here is my ultimate Zotero workflow:
1. Import only references into Zotero. Disable the PDF auto-save feature.
2. Download and save PDFs to your Dropbox folder (I use a subdirectory called PDFLibrary).
3. View the PDF file online through Dropbox using Firefox.
4. Right-click on the corresponding entry in Zotero and select Add attachment | Add link to current page.
This final step is the key. It will create a Zotero link to your PDF file in Dropbox. Double-clicking that attachment will open the web-Dropbox version of your PDF file (and preserves annotations!). Most importantly, this functionality will be preserved across Windows, OSX, Linux. And because your PDFs are in Dropbox, you can sync them with PDF Annotation apps on your phone or tablet. Now your PDF files and Zotero library will always be accessible and in sync.