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There used to be a menu item to export classpath variables. In 3.1 this is removed. There is no hit on "export classspath variable" in help. "Export preferences" is mentioned, but classpath variables are not explicitly excluded. If there is no intent to allow export/import of classpath variables then help text should say so ... the current test says that "all" preferences may be exported thru <file><export><preferences>.
Peter, what changed is the way how you trigger the export now. In the past this was done using the Export button on the page. This always triggered an export of ALL preferences. The export is now triggered using File->Export->Preferences. However, the fact that class path variable aren't exported anymore is a bug and I assigned the bug to the corresponding component.
*** Bug 97272 has been marked as a duplicate of this bug. ***