- Vaadin 6.4.6
- GAE SDK 1.3.8
- DataNucleus JDO 1.1.5 for Google App Engine (adapter version: 1.0.7)
- Vaadin Eclipse Plugin 1.2.1
- Google Plugin for Eclipse 1.3.3
- Eclipse Helios 3.6SR1
- Go to Project > Properties > Java Build Path
- Remove Web App Libraries
- Click Add JARs... , and add your Vaadin JAR from your project's war/WEB-INF/lib
The problem is in how GAE plugin interacts with the standard Eclipse Web Tools Platform (WTP). The Google plugin is designed to work primarily with its own non-WTP projects, and apparently does not handle WTP projects correctly. There is minimal documentation for using the Google plugin in existing projects (such as WTP), but it does not address this issue.
In summary, considering this a Google plugin WTP incompatibility, not a Vaadin plugin specific problem.