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The file org.eclipse.core.resources/scripts/buildExtraJAR.xml contains explicit list of paths for the javac command. There are at least two problems with it. First, due to the runtime split the following plugins have to be added to the path: org.eclipse.core.jobs org.eclipse.equinox.common Secondly, it won't work anyway as the jar files are generated with qualifier versions - the actual jar names are: org.eclipse.equinox.common_1.0.0.N20051121-0010.jar org.eclipse.osgi_3.2.0.N20051121-0010.jar and, of course, they change with every build.
Created attachment 30378 [details] Patch for the org.eclipse.core.resources Added a possible patch for this problem (used the approach from the org.eclipse.ant.core).
Thanks Oleg, patch released.