Check out the way that jetty shows for tutorial configurations. It's all done in Java code. Now that's interesting. It also accepts XML, which is good, but that's what everybody does.
I like exposing the container in this way. Instead of being forced to provide a config.xml or whatever, you can handle configuration however you'd like. So environment specific values, meta-information about the build, etc. can be determined or brought in programmatically. This seems very flexible to me, and could be customized for just about any need. I'll have to look into this some more.
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