I personally always have eclipse and maven building into different directories. I found in the past that having them build to the same directories got a little confusing if you start running maven commands like clean etc. - I think I ended up having to clean the projects in eclipse to get things built again. You would probably also end up having eclipse built rather than maven built classes in your JARs etc. Maybe not a big deal, but it made me feel a little uneasy not knowing exactly how things were built.
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