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During incremental compilation, AjState records classes generated from source files following the initial compile phase, but before weaving. (So that these can be passed to the weaver on a subsequent iteration if we need to reweave the world). During weaving of a given class file, the weaver may generate additional class files (for e.g. around closures) that get written to the output. If the orginal source file is deleted, these additional weaver generated classes are not deleted from the output since AjState does not know about them.
Fixed in tree. UnwovenClassFile.deleteRealFile now deletes the class file plus any $Ajc*.class extensions of it.