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Build I20070815-1600 but exists from initial implementation of bug 138599 in 3.3. Since bug 138599 has been implemented, deprecation message of classpath variables are stored in a JavaModelManager cache: 'deprecatedVariables'. This cache is populated while initializing the variable classpath initializer but is never freed when the variable is removed using JavaCore#removeClasspathVariable(String) API method...
Released for 3.4M2 in HEAD stream. The fix for this bug is available in patch attached to bug 186113.
(In reply to comment #1) Verified for 3.4 M2 using build I20070917-0010.