Q: Is it possible to open files, e.g. from my web browser, in the running instance of JabRef instead of opening a new instance?
A: Yes, if you activate the “Remote operation” option under Preferences -> Advanced. This option allows new instances of JabRef to detect the instance already running, and pass files to that instead of opening a new window.
Another dilemma I faced with JabRef was that whenever I tried importing directly from Google Scholar, it would open a new instance of the program instead of inserting the data into the instance that was already running.
Some explanation if this doesn’t make sense: An “instance” of a program refers to the running process; you can think of it as a window. When you open a Word document, it launches an instance of Word. If you open another Word document, a second instance of Word is launched to display that document. The most obvious reflection of this is that you will have two separate ‘windows’ of Word open on your screen. You can also launch the task manager (Ctrl+shift+escape) and see that there are two ‘WINWORD.EXE’ processes running.
With JabRef running and my desired bibliography database opened, I wanted to directly import results from Google Scholar. However, before toggling the setting mentioned above, JabRef was opening a separate instance for each citation I clicked, and duplicating my database each time. Now I have JabRef behaving nicely: each time I choose ‘Cite’ and ‘Import to RefMan’ for a Google Scholar result, it appends the data to my open database.
Of course, it’s also possible to use the built-in Google Scholar web search in JabRef, but I prefer using my web browser to get the ‘full’ experience. It also allows me to download PDFs if I don’t already have a copy.