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When using PDE's Automated Management of Dependencies feature the build.properties file keeps track of dependencies via the additional.bundles property key. Unfortunately, when you rename a dependent bundle the refactoring is not done to the additional.bundles property's value. This results in an error marker against the additional.bundles key in build.properties. The solution today is to manually remove the old bundle name and add the new bundle name. Please make the additional.bundles property value participate in the refactoring for renaming a bundle.
The relevant code is: org.eclipse.pde.internal.ui.refactoring.FindReferenceOperation The problem here I can see is tracking down dependants using the secondary classpath...
*** This bug has been marked as a duplicate of bug 261756 ***