Just because the IDEs can do deploys and/or that developers use that feature in their day to day development, doesn't mean that you need or should rely on that to do your production deploys.
For example, with Netbeans, you can leverage the Ant scripts that it generates to rebuild your application away from the developers and then deploy it to whereever and however you like, or you can integrate with any of the myriad of tools for that kind of thing.
At the moment, I'm just hand deploying EARs through the admin interface for our internal "public facing" day by day builds. Eventually we'll do some continuous integration tool set.
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