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Users who have projects configured to put .class files in same location as the .java files have to set the IDE to ignore .class files. This means they don't show up in the Files view, leading some users to think that the files haven't been compiled. Should just ignore .class files in the projects window by default.
For existing sources imported, *.class should be cleaned first. Users who wish to keep *.class alongside sources permanently (incl. making corresponding build script changes) can either ignore *.class in System Settings (applies to Projects and Files tabs both) or not. *** This issue has been marked as a duplicate of 48198 ***
This issue was solved long time ago. Because nobody has reopened it neither added comments, we are verifying/closing it now. If you are still able to reproduce the problem, please reopen. Thanks in advance.