Any luck with this?
I think I have the same problem. Basically, I'm trying to set up a development environment where no IDE-specific stuff gets into the repository, only pom:s and code. It works great with Netbeans, but Eclipse doesn't seem to recognize that my projects are Webapps, so I can't deploy them, even though Maven builds a war as well as exploded war in target.
Please let me know if you solved your problem!