The jabref version bump got stuck for some while. see bug #385751 I suggest to provide app-text/jabref-bin, which checks dependencies and copies the .jar file to a systemwide directory like /usr/share/bin(?) Reproducible: Always
I have added the current stable version (app-text/jabref-2.9.2) to the tree. Please give it a try and let us know if you run into any issues.
Working on jabref-2.10_beta3, which will make this bug obsolete.
jabref-2.10_beta3 in tree.