Is it completely up to the developers/deployers wether the necessary resources get declared in the server or in the application?
This is correct.
Is it just for convenience, so that deployer doesn't have to unpack the WAR?
No, this has nothing to do with unpacking WAR files.
Or -- like someone stated on this list (to my confusion) -- that the server.xml Resource element and the web.xml resource-ref have a relation that is similar to that of an implementation class instance and an interface?
This is an apt analogy. The server.xml sets up the actual resource (often in the <GlobalNamingResources> section), then allows the application to use it (by adding a <ResourceLink> section in the <Context> where you want to use it). The webapp signifies its desire to use that resource by including a complimentary <resource-ref> section in the deployment descriptor.
-chris
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