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Build 20011219 + JDTCORE official patch After importing all plugin projects in a fresh new workspace (using the pde import tool), org.eclipse.ui does not have correct project references (it actually has none). It does not matter whether importing in source/binary form.
Seems it can occur if at some point the classpath is set in a mode where resources cannot be touched. From there on, project references maybe left inconsistent since further opening of the buildpath wizard (and no change is performed, just press ok) will be optimized out (thought that the classpath is not actually changed). Fixed