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wstool merge --help gives you the options it has. --merge-keep does not quite do what you want, it does not detect that a package already exists in /opt/ros/groovy.

You could wget the url into a local file, then prune entries yourself, either manually or via a script. In python you could do that by yaml-parsing the rosinstall file you got via wget, giving you a list of dicts, then getting all packages you have installed, and removing those entries from the list, and then writing the remaining items into a file.

If enough people wanted this (indicated by +1 comments on my answer, or on a ticket on vcstools/rosinstall at github), we could maybe include such features, though probably into roslocate instead.