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



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