The Servlet Specification 3.0, section 10.5, defines WEB-INF/lib/*.jar as the location for libraries embedded into a WAR. So if you want to be container independent, it seems you'll have to stick with that. Or maybe use an EAR instead of a WAR.
By the way, I don't really see the problem: As long as we're talking about a single deployment unit (i.e. your WAR with 50 JARs), the internal structure of that WAR is just an implementation detail you shouldn't have to worry about.
I suspect the real problem you're trying to solve is organizing your workspace or your build process. Maybe Maven can help.
Regards,
Harald
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