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The build starts before the Java UI plugin is activated and the class path initialized. Workaround is to rebuild again.
This is what happens: (code in org.eclipse.jdt.ui.examples.projects) - A project is created with natures specified in the plugin.xml (->includes jdt nature) - Project content, including the .classpath file is imported (all in a workspacerunnable) - This overwrite the existing classpath file. As the bug describes, the build triggered by the import a rebuild does not use the new .classpath file. - Rebuild: Errors are gone moving to jdt.core The change of .classpath should retrigger the build.
It is critical since this is part of the getting started experience.
This is our well-known defect with unitialized classpath variables.
Fixed by introducing classpath variable initializers (also see bug 3303).