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When you do File->Export->Preferences and invoke "Export all" verses invoking "Choose specific preferences to export" and choosing all the available check boxes doesn't produce the same result. This is confusing to users and indicates that there is a check box missing for whatever is exported in the first case but not in the second case. Please add more check boxes, even just an other category, to represent the missing preferences that are exported only in the first case. Specifically I want to be able to export my preferences without exporting the JREs since those will be specific to my machine.
It shouldn't. The preference transfers only cover preference groups contributed by plug-ins. For this to be the case everyone would need to provide transfers for all of thier preferences. Some should not be exported anyways as they are internal but more use of this mechanism would give a better result.