Sorry, I don't know anything about how emacs-eclim is setup, so
getting in touch with one of the authors of that project, or a
knowledgable user, would be your best bet.
With regards to the command, it almost certainly should be attempting
to run the 'eclim' shell script and not java. Perhaps there is some
config that tells emacs-eclim where the 'eclim' script is, but for
some reason that config is set to /usr/bin/java instead?
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eric