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Please follow this (and also others) coding guideliness to make it easier for other people to read the code.
Radime, this issue is not very specific. Are there any particular classes you have in mind?
org.netbeans.modules.j2ee.deployment.config.ui.Braindead/Complex/Simple/Fixed probably it would be best to write some rule for bug finder such as PMD.
Assigning to Nam.
Make Braindead/Complex/Simple/Fixed into static inner classes.