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HEAD The problem markers generated for references to deprecated classpath variables currently have ERROR severity (at least when build path error severity is set to Error). The problem is maybe in JavaProject.createClasspathProblemMarker(IJavaModelStatus) where the "switch (status.getCode())" does not have a special case for IJavaModelStatusConstants.DEPRECATED_VARIABLE and thus the JavaCore.CORE_INCOMPLETE_CLASSPATH option is consulted for the severity. Adding case IJavaModelStatusConstants.DEPRECATED_VARIABLE : severity = IMarker.SEVERITY_WARNING; break; fixed it for me, but I'm not sure if that's the correct fix.
Actually, you should also set the path argument to the marker (like in the default clause), so that a quick fix (e.g. for JUNIT_HOME/***) can find out whether it is applicable.
Created attachment 57926 [details] Proposed patch
Released for 3.3 M5 in HEAD stream.
Contrasted the test case results for M5 candidate (v_734) and v_733. Verified for 3.3 M5 using build I20070205-1824.