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If you tell the IDe to clean or clean All, it will only remove the class files that match source files it has. It will not remove all class files from the directory as I believe it should. clearly this is intentional behavior because its not simply doing a del *.class as one would expect. So at the very least their should be some indication that their are unknown classes in the classes directory so when you run your program and its doing strange stuff, you know that their are some extra classes hanging around. For me this problem occurs when you compile, then rename a file. The already generated class file is never cleaned up. causes problems when your refactoring the code.
Also I noticed that if the file is set not to compile, it also will not clean. I guess thats not entirely bad. Be nice to know at a glance which files are set not to compile (icon). Seems like an obvious feature. Maybe its already under consideration. If so let me know where I can read about such planned enhancements so I dont post again on this topic.
See issue 8905 *** This issue has been marked as a duplicate of 8905 ***
I tried not to report a duplicate bug, but I searched for 'clean not' but nothing came up. perhaps the searching mechanism has a bug too...
File a bug against the searching mechanism :-)