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Unchecking the “show derived resources” box does not remove the .class files from the “Matching Resources” section. All it does is remove the path to the .class file in the “In Folders” section.
Hmm, on my end it actually removed the .class listings, but it’s possible my project setup is different. Regardless, this setting is provided by the base Eclipse JDT install, so I don’t know that much about that particular resource window, Im sorry.