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The plugin import tool does not set the project references. This is critically important on projects that have been expanded to source because the build order is incorrect. For example, I imported all of the plugins as source, and the first plugin that was built was org.eclipse.pde. It most likely should have been something like org.eclipse.core.runtime.
This looks like coming from 6100. Should work in the latest drop of eclipse (11121)
I'm not sure I understand your comment about 6100. I have tried this with the 20011122 build. The project references were not set.
finally works in 11127