I don't think the directory should be changed.
I think nautilus should call the JVM using the current directory,
but it seems to be calling it using my home (/home/my-user).

When I launch java in the terminal, the JVM thinks the current
directory is the current directory.

When I launch java through nautilus, the JVM thinks the current
directory is /home/my-user, regardless of the current directory.
In this case, launching through nautilus, printing the current directory
will always print "/home/my-user", no matter which directory
my .jar file actually is in.

-- 
jvm receives wrong path
https://bugs.launchpad.net/bugs/234777
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