Third try: if I explicitly set classpath with this line
java -cp
/usr/share/beast-mcmc/lib/beast.jar:/usr/share/java/jam.jar:/usr/share/java/jdom1.jar:/usr/share/java/jebl.jar:/usr/share/java/commons-math.jar
dr.app.beast.BeastMain
then the program starts, accept the Flu.xml file and starts thinking,
writing some funny numbers on the screen (which I assume is a method to
say me "Hay man, things are wonderful here and I'm working happily").
The command line:
java -cp
/usr/share/java/jam.jar:/usr/share/java/jdom1.jar:/usr/share/java/jebl.jar:/usr/share/java/commons-math.jar
-jar /usr/share/beast-mcmc/lib/beast.jar
(which in my opinion should be equivalent to the previous, but clearly
is not) doesn't work. The program still fails finding the same class
from jebl. Probably the mechanism the virtual machine uses to search
classes when invoked with the "-jar" option isn't totally clear to me
(nevertheless, I'm sure that the Class-Path field in the manifest has
some meaning, because if I take it out from some JAR that actually works
with -jar, it doesn't work anymore).