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Rewrite all SystemOption settings to common JavaBean and use Settings Convertors API. Where possible keep backward compatability. http://www.netbeans.org/download/dev/javadoc/SettingsAPIs/org/netbeans/spi/settings/doc-files/api.html
Another even better approach is to decompose settings objects to individual properties and store these in Registry Contexts. It's simpler. The Registry API will be introduced in NB 4.0 platform.
Not there yet, not sure when it will be.