Tyler wrote:

The entire contents of the script that is supposed to start everything is:

jre -cp arlequin.jar -cp swingall.jar arlequin.ArlequinApp

The double "-cp" (CLassPath) options looks dodgy to me. I thought you could only have one "cp" option (but that one option could have a number of entries in it).

You could try changing it to:
java -cp arlequin.jar:swingall.jar arlequin.ArlequinApp

or possibly

java -jar arlequin.jar


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