I’ve no idea why Eclipse is including your target directory within the WEB-INF/classes folder. Do you use m2e (M2Eclipse) or the maven-eclipse-plugin? With m2e you could try to “Update project configuration” and do a full clean. This may help. But it may also be caused by your pom.xml or some maven plugin that is misbehaving.
However I thought about this issue again and I think I will change the PrettyFaces scanning code to NEVER process a class twice in the annotation discovery process. This will never make sense and will always lead to exceptions like you got them.
I’ll keep you up to date regarding this.
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