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I notice the wst.standard.schemas bundle is also packaged as a "source bundle". Since this is a resource-only project, that doesn't make sense, and these (the jst one too) should be marked as "no source" in their build.properties.
Here's a few more org.eclipse.jpt.doc.user.source_1.0.100.v200805280000.jar org.eclipse.jst.ws.axis2.ui.doc.user.source_1.0.0.v200805211529.jar org.eclipse.wst.jsdt.doc.source_1.0.0.v200805302104.jar Though, oddly, the jsdt one doesn't have a regular one.
For the record, the line that needs to be added to the build.properties file is generateSourceBundle=false
I've fixed following: wst.standard.schemas jst.standard.schemas org.eclipse.jst.ws.axis2.ui.doc.user.source_1.0.0.v200805211529.jar org.eclipse.wst.jsdt.doc.source_1.0.0.v200805302104.jar And, opened a bug for org.eclipse.jpt.doc.user.source_1.0.100.v200805280000.jar