If you ran the commands in my code block in that exact order, and still have the same results, then you should probably send-pr about it. Remember that this issue has
nothing to do with Eclipse, and is a problem with the libgnome port, not Eclipse. The problem is simply with a dependency for Eclipse. Going to the Eclipse folks will yield no results. Instead, go to the FreeBSD GNOME folks via a send-pr. You may want to quote the URL to this thread in the PR text so that anyone looking over it can see what you've already tried, as the advice I gave you is usually the first advice given to anyone with problems such as yours by a port maintainer.