After due reflection, I think that actually setting up an archetype with non-standard directory layout isn't really a good idea.
I'll admit that one of the first things that kept me from adopting Maven initially was its insistence on its own special directory structure. The second thing being that unlike Ant, you couldn't see what the rules being executed were.
But I've since learned to accept it. For a couple of reasons.
1. It's consistent. Every (standard) Maven project in the world has the same directory structure. That means that if I pass a project to someone in Outer Mongolia, they will instantly know where to find stuff without wasting time searching.
2. It's simple. The very thing that put me off about Maven - the fact that it does things by "magic" instead of explicitly-written rules means that you don't waste time setting up build rules (or in this case, POM overrides). The fact that the magic tools don't have to be told where the source, resources and other build inputs are located is a further benefit.
3. It's authoritative. Several new build systems have been developed since Maven that act on the same general
philosophy. I'd expect them to also follow the same general organization, thus reducing their learning curves and helping support their own adherence to the first 2 items listed above.
I'm NOT saying to turn the shop upside down and re-code all the builds willy-nilly. But it
would be a good idea to migrate to standard directory structure as new builds are created (which is what archetypes are for). It's not so burdensome to have 2 sets of rules rather than 1 while in transition, and if you already had a consistent structure, it shouldn't even be that hard to put together a migration script to be used as projects come up for maintenance.
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