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This bug is a consequence of bug 33475. In that bug the classpath variables were broken when related to link files. The strange thing is that the classpath was also broken for a project that did not depend on the "link classpath variable". Here's an example to clarify: 1) I have a link file pointing to a GEF install. 2) No binary projects exist in the workspace. 3) Plugin A requires GEF. 4) Plugin B only requires Eclipse plugins and uses the ECLIPSE_HOME variable. Plugin A classpath is broken due to bug 33475. Plugin B classpath is also broken even though it does not depend on GEF.
The symptoms you're seeing in plugin B are actually a consequence of bug 33475. Fixing bug 33475 fixes plugin B classpath. *** This bug has been marked as a duplicate of 33475 ***