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Apple moved the javaws.jar and plugin.jar files to /System/Library/Frameworks/JavaVM.framework/Resources/Deploy.bundle/Contents/Home/lib in Java 6. Eclipse does not (currently) support traversing into bundles, so it is not possible to use the Eclipse GUI to add these libraries to the default JDK classpath. However, they can be manually added by editing the libraryInfos.xml configuration file:

<workspace_root>/.metadata/.plugins/org.eclipse.jdt.launching/libraryInfos.xml

Add entries for javaws.jar and plugin.jar to the <libraryInfo> elements for JDK 1.6/1.6.0:

<entry path="/System/Library/Frameworks/JavaVM.framework/Resources/Deploy.bundle/Contents/Home/lib/plugin.jar"/>
<entry path="/System/Library/Frameworks/JavaVM.framework/Resources/Deploy.bundle/Contents/Home/lib/javaws.jar"/>