The many jars are sadly partly incompatible when versions differ too much. I had some real bad time when I used Taverna with mixtures of self-created, official Debian and shipping jars.
I hope that I don't sound too negative when I say that Jalview will not be DFSG compatible with us for quite some time. Would something shipping extra jars be redistributable in the non-free section? Then I am opting quite much for that. We'd remove from the sources what is removable and leave the rest in for now, in order to have something functional to start with. Those would then shrink over time as more and more becomes available as Debian packages that was before shipped as a Jar. Best, Steffen -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org