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In a CDT development environment, you can browser the source code of most Eclipse Platform classes that CDT directly or indirectly uses, but not classes in org.eclipse.e4.* packages (such as org.eclipse.e4.ui.model.application.ui.basic.MPart).
New Gerrit change created: https://git.eclipse.org/r/125756
Nate, I can't find it now, but there is (or at least was) a bug in Eclipse PDE related to having features causing this kind of problem. Can you try and remove all feature projects from your workspace (I think closing them is sufficient).
Hmm. Never mind, Bug 507098 seems to be the one and it has been fixed for a while now. That said, what you are describing is still a bug in PDE, rather than an error in CDT, however a workaround in CDT sounds reasonable.