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I do extensively use NetBeans' "Fix uses..." feature to clean the code. Currently NetBeans searches and replaces also class names inside the comments. This causes some problems for example in annotated docblocks where the docblock may contain some special class-like code. One example is Doctrine MongoDB ODM annotations: /** * @MongoDB\ReferenceOne(targetDocument="SomeOther\Namespace\Document") */ Here, NetBeans replaces also text inside targetDocument="" even it should not. I would suggest that Fix uses... feature would not touch code comments at all.