[protege-owl] Remaining codes

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[protege-owl] Remaining codes

zze-SIA Jamal RD-BIZZ-SOP
Remaining codes

Hi,
I've noticed that even if i modify my ontology using the protege GUI there is still some code remaining of previous manipulations. Something like

<superclass>
        <subSuperClass>
                <misplacedClass>
                        <MyClass>
                                ……
                        </MyClass>
                </misplacedClass>
        </subSuperClass>
</superclass>

When i intentionally deleted <misplacedClass> definitions. Is there a tool to clean up all undetermined or unused classes ?