I love Vaadin but it is a bit broken in regards to how it deals with maven.
Maven is a beast, but if one is doing any form of serious java development it is really the only game in town. There is really no excuse if your doing any serious Java development for not using maven.
There is a convention for where to place generated sources for maven projects: target/generated-sources
Maybe having the archetype behave this way is OK because it gets the project up and running quickly, but it is definitely a bad practice IMHO.