Yes, that's more or less what I'm doing, only I'm using the native API org.glassfish.api.embedded.*, as I could not find any usable documentation for the javax.ejb.embeddable.EJBContainer API.
I agree that a classpath composed from multiple directories [i]should[/i] work, but I believe it does not.
I work with m2eclipse, so it's not a big deal running a Maven build before running (or debugging) my integration tests in Eclipse interactively. Surely you do not want to run all your integration tests automatically when saving a source file in Eclipse?
Regards,
Harald
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