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I have a java project open, and whenever I open the jumpto-dialog to open a file, it lists the .class file for the class before the .java file... I don't think there is a lot of users out there that normally open a .class file in the ide, so I would say that giving the .java file as the first file listed would improve the user experience...
(See analogous issue #44310, classified as a DEFECT.) Works for me on NBM projects. SearchWorker.findFiles does check SourceGroup.contains, which normally will exclude SharabilityQuery.NOT_SHARABLE files and subfolders, such as build/, so the *.class files should not be presented at all. (Perhaps more importantly than order of listing, this improves the search speed.) Certain project types may fail to indicate sharability of some subfolders, in particular freeform projects. I will make sure that is filed separately.