The current J2SE build sometimes fails to overwrite some files from the bootstrap compile. The following files from rt.jar and tools.jar have been identified as being left over from a bootstrap build:

com/sun/tools/javac/jvm/ClassWriter.class
com/sun/tools/javac/util/Name$Table.class
com/sun/tools/javadoc/AnnotationValueImpl$1.class
com/sun/tools/javadoc/Comment$1CommentStringParser.class
com/sun/tools/javadoc/DocletInvoker$1.class
com/sun/tools/javadoc/JavadocClassReader$1.class
com/sun/tools/javadoc/JavadocEnter$1.class
com/sun/tools/javadoc/JavadocMemberEnter$1.class
com/sun/tools/javadoc/JavadocTodo$1.class
com/sun/tools/javadoc/Messager$1.class
com/sun/tools/javadoc/Messager$2.class
java/lang/Class$1.class
java/lang/Class$2.class
java/lang/Class$3.class
java/lang/ClassLoader$1.class
java/lang/ClassLoader$2.class
java/lang/ClassLoader$3.class
java/lang/FloatingDecimal$1.class
java/lang/String$1.class
java/lang/ThreadLocal$1.class
java/lang/ref/Reference$1.class
java/lang/ref/ReferenceQueue$1.class
java/util/AbstractList$1.class
java/util/AbstractMap$1.class
java/util/AbstractMap$2.class
java/util/AbstractMap$3.class
java/util/AbstractMap$4.class
java/util/Collections$1.class
java/util/Collections$2.class
java/util/Collections$3.class
java/util/Collections$4.class
java/util/Collections$5.class
java/util/Collections$6.class
java/util/Collections$7.class
java/util/Collections$8.class
java/util/HashMap$1.class
java/util/Hashtable$1.class
java/util/LinkedHashMap$1.class
java/util/SubList$1.class
java/util/Vector$1.class
java/util/prefs/FileSystemPreferences$1.class
java/util/prefs/FileSystemPreferences$10.class
java/util/prefs/FileSystemPreferences$11.class
java/util/prefs/FileSystemPreferences$12.class
java/util/prefs/FileSystemPreferences$13.class
java/util/prefs/FileSystemPreferences$14.class
java/util/prefs/FileSystemPreferences$2.class
java/util/prefs/FileSystemPreferences$3.class
java/util/prefs/FileSystemPreferences$4.class
java/util/prefs/FileSystemPreferences$5.class
java/util/prefs/FileSystemPreferences$6.class
java/util/prefs/FileSystemPreferences$7.class
java/util/prefs/FileSystemPreferences$8.class
java/util/prefs/FileSystemPreferences$9.class
javax/pack/Attribute.class
javax/pack/BandStructure.class
javax/pack/Constants.class

To help diagnose this in the future, javac should be capable of placing a marker attribute into all generated class files. We can use one marker during bootstrapping and another (or none) during the rebuild. Any bits remaining with the bootstrap marker are bad.