Java: Update integration test expected output.

Author: michaelnebel

java/ql/integration-tests/java/query-suite/java-code-quality-extended.qls.expected

@@ -1,61 +1,122 @@
 ql/java/ql/src/Advisory/Declarations/MissingOverrideAnnotation.ql
+ql/java/ql/src/Advisory/Declarations/NonFinalImmutableField.ql
+ql/java/ql/src/Advisory/Declarations/NonPrivateField.ql
 ql/java/ql/src/Advisory/Documentation/ImpossibleJavadocThrows.ql
+ql/java/ql/src/Advisory/Documentation/MissingJavadocMethods.ql
+ql/java/ql/src/Advisory/Documentation/MissingJavadocParameters.ql
+ql/java/ql/src/Advisory/Documentation/MissingJavadocReturnValues.ql
+ql/java/ql/src/Advisory/Documentation/MissingJavadocThrows.ql
+ql/java/ql/src/Advisory/Documentation/MissingJavadocTypes.ql
 ql/java/ql/src/Advisory/Documentation/SpuriousJavadocParam.ql
+ql/java/ql/src/Advisory/Java Objects/AvoidCloneMethodAccess.ql
+ql/java/ql/src/Advisory/Java Objects/AvoidCloneOverride.ql
+ql/java/ql/src/Advisory/Java Objects/AvoidCloneableInterface.ql
+ql/java/ql/src/Advisory/Java Objects/AvoidFinalizeOverride.ql
+ql/java/ql/src/Advisory/Naming/NamingConventionsConstants.ql
+ql/java/ql/src/Advisory/Naming/NamingConventionsMethods.ql
+ql/java/ql/src/Advisory/Naming/NamingConventionsPackages.ql
+ql/java/ql/src/Advisory/Naming/NamingConventionsRefTypes.ql
+ql/java/ql/src/Advisory/Naming/NamingConventionsVariables.ql
+ql/java/ql/src/Advisory/Statements/MissingDefaultInSwitch.ql
+ql/java/ql/src/Advisory/Statements/OneStatementPerLine.ql
+ql/java/ql/src/Advisory/Statements/TerminateIfElseIfWithElse.ql
+ql/java/ql/src/Advisory/Types/GenericsConstructor.ql
+ql/java/ql/src/Advisory/Types/GenericsReturnType.ql
+ql/java/ql/src/Advisory/Types/GenericsVariable.ql
 ql/java/ql/src/Compatibility/JDK9/JdkInternalAccess.ql
 ql/java/ql/src/Compatibility/JDK9/UnderscoreIdentifier.ql
+ql/java/ql/src/DeadCode/DeadClass.ql
+ql/java/ql/src/DeadCode/DeadEnumConstant.ql
+ql/java/ql/src/DeadCode/DeadField.ql
+ql/java/ql/src/DeadCode/DeadMethod.ql
 ql/java/ql/src/DeadCode/UselessParameter.ql
 ql/java/ql/src/Language Abuse/EmptyMethod.ql
 ql/java/ql/src/Language Abuse/IterableIterator.ql
 ql/java/ql/src/Language Abuse/LabelInSwitch.ql
+ql/java/ql/src/Language Abuse/OverridePackagePrivate.ql
+ql/java/ql/src/Language Abuse/TypeVarExtendsFinalType.ql
 ql/java/ql/src/Language Abuse/TypeVariableHidesType.ql
 ql/java/ql/src/Language Abuse/UselessNullCheck.ql
 ql/java/ql/src/Language Abuse/UselessTypeTest.ql
 ql/java/ql/src/Language Abuse/WrappedIterator.ql
+ql/java/ql/src/Likely Bugs/Arithmetic/BadAbsOfRandom.ql
 ql/java/ql/src/Likely Bugs/Arithmetic/ConstantExpAppearsNonConstant.ql
 ql/java/ql/src/Likely Bugs/Arithmetic/IntMultToLong.ql
 ql/java/ql/src/Likely Bugs/Arithmetic/LShiftLargerThanTypeWidth.ql
+ql/java/ql/src/Likely Bugs/Arithmetic/MultiplyRemainder.ql
+ql/java/ql/src/Likely Bugs/Arithmetic/RandomUsedOnce.ql
 ql/java/ql/src/Likely Bugs/Arithmetic/WhitespaceContradictsPrecedence.ql
+ql/java/ql/src/Likely Bugs/Cloning/MissingCallToSuperClone.ql
+ql/java/ql/src/Likely Bugs/Cloning/MissingMethodClone.ql
 ql/java/ql/src/Likely Bugs/Collections/ArrayIndexOutOfBounds.ql
 ql/java/ql/src/Likely Bugs/Collections/ContainsTypeMismatch.ql
+ql/java/ql/src/Likely Bugs/Collections/IteratorRemoveMayFail.ql
 ql/java/ql/src/Likely Bugs/Collections/ReadOnlyContainer.ql
 ql/java/ql/src/Likely Bugs/Collections/RemoveTypeMismatch.ql
 ql/java/ql/src/Likely Bugs/Collections/WriteOnlyContainer.ql
 ql/java/ql/src/Likely Bugs/Comparison/CompareIdenticalValues.ql
+ql/java/ql/src/Likely Bugs/Comparison/CovariantCompareTo.ql
+ql/java/ql/src/Likely Bugs/Comparison/CovariantEquals.ql
 ql/java/ql/src/Likely Bugs/Comparison/EqualsArray.ql
 ql/java/ql/src/Likely Bugs/Comparison/HashedButNoHash.ql
 ql/java/ql/src/Likely Bugs/Comparison/IncomparableEquals.ql
+ql/java/ql/src/Likely Bugs/Comparison/InconsistentCompareTo.ql
 ql/java/ql/src/Likely Bugs/Comparison/InconsistentEqualsHashCode.ql
 ql/java/ql/src/Likely Bugs/Comparison/MissingInstanceofInEquals.ql
 ql/java/ql/src/Likely Bugs/Comparison/RefEqBoxed.ql
+ql/java/ql/src/Likely Bugs/Comparison/StringComparison.ql
 ql/java/ql/src/Likely Bugs/Comparison/UselessComparisonTest.ql
 ql/java/ql/src/Likely Bugs/Comparison/WrongNanComparison.ql
+ql/java/ql/src/Likely Bugs/Concurrency/CallsToConditionWait.ql
 ql/java/ql/src/Likely Bugs/Concurrency/CallsToRunnableRun.ql
+ql/java/ql/src/Likely Bugs/Concurrency/DateFormatThreadUnsafe.ql
 ql/java/ql/src/Likely Bugs/Concurrency/DoubleCheckedLocking.ql
 ql/java/ql/src/Likely Bugs/Concurrency/DoubleCheckedLockingWithInitRace.ql
+ql/java/ql/src/Likely Bugs/Concurrency/FutileSynchOnField.ql
 ql/java/ql/src/Likely Bugs/Concurrency/NonSynchronizedOverride.ql
+ql/java/ql/src/Likely Bugs/Concurrency/NotifyNotNotifyAll.ql
 ql/java/ql/src/Likely Bugs/Concurrency/ScheduledThreadPoolExecutorZeroThread.ql
+ql/java/ql/src/Likely Bugs/Concurrency/SleepWithLock.ql
+ql/java/ql/src/Likely Bugs/Concurrency/StartInConstructor.ql
 ql/java/ql/src/Likely Bugs/Concurrency/SynchOnBoxedType.ql
 ql/java/ql/src/Likely Bugs/Concurrency/SynchSetUnsynchGet.ql
+ql/java/ql/src/Likely Bugs/Concurrency/SynchWriteObject.ql
+ql/java/ql/src/Likely Bugs/Finalization/NullifiedSuperFinalize.ql
+ql/java/ql/src/Likely Bugs/Frameworks/JUnit/BadSuiteMethod.ql
 ql/java/ql/src/Likely Bugs/Frameworks/JUnit/JUnit5MissingNestedAnnotation.ql
+ql/java/ql/src/Likely Bugs/Frameworks/Swing/BadlyOverriddenAdapter.ql
 ql/java/ql/src/Likely Bugs/Inheritance/NoNonFinalInConstructor.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/ContainerSizeCmpZero.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/ContradictoryTypeChecks.ql
+ql/java/ql/src/Likely Bugs/Likely Typos/DangerousNonCircuitLogic.ql
+ql/java/ql/src/Likely Bugs/Likely Typos/EqualsTypo.ql
+ql/java/ql/src/Likely Bugs/Likely Typos/HashCodeTypo.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/MissingFormatArg.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/MissingSpaceTypo.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/SelfAssignment.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/StringBufferCharInit.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/SuspiciousDateFormat.ql
+ql/java/ql/src/Likely Bugs/Likely Typos/ToStringTypo.ql
 ql/java/ql/src/Likely Bugs/Likely Typos/UnusedFormatArg.ql
 ql/java/ql/src/Likely Bugs/Nullness/NullAlways.ql
 ql/java/ql/src/Likely Bugs/Nullness/NullExprDeref.ql
 ql/java/ql/src/Likely Bugs/Nullness/NullMaybe.ql
+ql/java/ql/src/Likely Bugs/Reflection/AnnotationPresentCheck.ql
 ql/java/ql/src/Likely Bugs/Resource Leaks/CloseReader.ql
 ql/java/ql/src/Likely Bugs/Resource Leaks/CloseSql.ql
 ql/java/ql/src/Likely Bugs/Resource Leaks/CloseWriter.ql
+ql/java/ql/src/Likely Bugs/Serialization/IncorrectSerialVersionUID.ql
+ql/java/ql/src/Likely Bugs/Serialization/IncorrectSerializableMethods.ql
+ql/java/ql/src/Likely Bugs/Serialization/MissingVoidConstructorOnExternalizable.ql
+ql/java/ql/src/Likely Bugs/Serialization/MissingVoidConstructorsOnSerializable.ql
+ql/java/ql/src/Likely Bugs/Serialization/NonSerializableInnerClass.ql
+ql/java/ql/src/Likely Bugs/Serialization/ReadResolveObject.ql
 ql/java/ql/src/Likely Bugs/Statements/ContinueInFalseLoop.ql
+ql/java/ql/src/Likely Bugs/Statements/MissingEnumInSwitch.ql
 ql/java/ql/src/Likely Bugs/Statements/PartiallyMaskedCatch.ql
 ql/java/ql/src/Likely Bugs/Statements/UseBraces.ql
 ql/java/ql/src/Likely Bugs/Termination/ConstantLoopCondition.ql
+ql/java/ql/src/Likely Bugs/Termination/SpinOnField.ql
 ql/java/ql/src/Performance/InefficientEmptyStringTest.ql
 ql/java/ql/src/Performance/InefficientKeySetIterator.ql
 ql/java/ql/src/Performance/InefficientOutputStream.ql
@@ -64,6 +125,7 @@ ql/java/ql/src/Performance/InnerClassCouldBeStatic.ql
 ql/java/ql/src/Performance/NewStringString.ql
 ql/java/ql/src/Performance/StringReplaceAllWithNonRegex.ql
 ql/java/ql/src/Violations of Best Practice/Boxed Types/BoxedVariable.ql
+ql/java/ql/src/Violations of Best Practice/Dead Code/CreatesEmptyZip.ql
 ql/java/ql/src/Violations of Best Practice/Dead Code/DeadRefTypes.ql
 ql/java/ql/src/Violations of Best Practice/Dead Code/InterfaceCannotBeImplemented.ql
 ql/java/ql/src/Violations of Best Practice/Dead Code/UnreadLocal.ql
@@ -73,10 +135,12 @@ ql/java/ql/src/Violations of Best Practice/Exception Handling/IgnoreExceptionalR
 ql/java/ql/src/Violations of Best Practice/Exception Handling/NumberFormatException.ql
 ql/java/ql/src/Violations of Best Practice/Implementation Hiding/AbstractToConcreteCollection.ql
 ql/java/ql/src/Violations of Best Practice/Implementation Hiding/ExposeRepresentation.ql
+ql/java/ql/src/Violations of Best Practice/Implementation Hiding/GetClassGetResource.ql
 ql/java/ql/src/Violations of Best Practice/Implementation Hiding/VisibleForTestingAbuse.ql
 ql/java/ql/src/Violations of Best Practice/Naming Conventions/AmbiguousOuterSuper.ql
 ql/java/ql/src/Violations of Best Practice/Naming Conventions/ConfusingMethodNames.ql
 ql/java/ql/src/Violations of Best Practice/Naming Conventions/ConfusingOverloading.ql
+ql/java/ql/src/Violations of Best Practice/Naming Conventions/FieldMasksSuperField.ql
 ql/java/ql/src/Violations of Best Practice/Naming Conventions/LocalShadowsFieldConfusing.ql
 ql/java/ql/src/Violations of Best Practice/Naming Conventions/SameNameAsSuper.ql
 ql/java/ql/src/Violations of Best Practice/Records/IgnoredSerializationMembersOfRecordClass.ql
@@ -87,4 +151,5 @@ ql/java/ql/src/Violations of Best Practice/Undesirable Calls/CallsToStringToStri
 ql/java/ql/src/Violations of Best Practice/Undesirable Calls/CallsToSystemExit.ql
 ql/java/ql/src/Violations of Best Practice/Undesirable Calls/DefaultToString.ql
 ql/java/ql/src/Violations of Best Practice/Undesirable Calls/DoNotCallFinalize.ql
+ql/java/ql/src/Violations of Best Practice/Undesirable Calls/NextFromIterator.ql
 ql/java/ql/src/Violations of Best Practice/Undesirable Calls/PrintLnArray.ql

java/ql/integration-tests/java/query-suite/not_included_in_qls.expected

@@ -1,25 +1,3 @@
-ql/java/ql/src/Advisory/Declarations/NonFinalImmutableField.ql
-ql/java/ql/src/Advisory/Declarations/NonPrivateField.ql
-ql/java/ql/src/Advisory/Documentation/MissingJavadocMethods.ql
-ql/java/ql/src/Advisory/Documentation/MissingJavadocParameters.ql
-ql/java/ql/src/Advisory/Documentation/MissingJavadocReturnValues.ql
-ql/java/ql/src/Advisory/Documentation/MissingJavadocThrows.ql
-ql/java/ql/src/Advisory/Documentation/MissingJavadocTypes.ql
-ql/java/ql/src/Advisory/Java Objects/AvoidCloneMethodAccess.ql
-ql/java/ql/src/Advisory/Java Objects/AvoidCloneOverride.ql
-ql/java/ql/src/Advisory/Java Objects/AvoidCloneableInterface.ql
-ql/java/ql/src/Advisory/Java Objects/AvoidFinalizeOverride.ql
-ql/java/ql/src/Advisory/Naming/NamingConventionsConstants.ql
-ql/java/ql/src/Advisory/Naming/NamingConventionsMethods.ql
-ql/java/ql/src/Advisory/Naming/NamingConventionsPackages.ql
-ql/java/ql/src/Advisory/Naming/NamingConventionsRefTypes.ql
-ql/java/ql/src/Advisory/Naming/NamingConventionsVariables.ql
-ql/java/ql/src/Advisory/Statements/MissingDefaultInSwitch.ql
-ql/java/ql/src/Advisory/Statements/OneStatementPerLine.ql
-ql/java/ql/src/Advisory/Statements/TerminateIfElseIfWithElse.ql
-ql/java/ql/src/Advisory/Types/GenericsConstructor.ql
-ql/java/ql/src/Advisory/Types/GenericsReturnType.ql
-ql/java/ql/src/Advisory/Types/GenericsVariable.ql
 ql/java/ql/src/AlertSuppression.ql
 ql/java/ql/src/AlertSuppressionAnnotations.ql
 ql/java/ql/src/Architecture/Dependencies/MutualDependency.ql
@@ -31,10 +9,6 @@ ql/java/ql/src/Architecture/Refactoring Opportunities/HubClasses.ql
 ql/java/ql/src/Architecture/Refactoring Opportunities/InappropriateIntimacy.ql
 ql/java/ql/src/Complexity/BlockWithTooManyStatements.ql
 ql/java/ql/src/Complexity/ComplexCondition.ql
-ql/java/ql/src/DeadCode/DeadClass.ql
-ql/java/ql/src/DeadCode/DeadEnumConstant.ql
-ql/java/ql/src/DeadCode/DeadField.ql
-ql/java/ql/src/DeadCode/DeadMethod.ql
 ql/java/ql/src/DeadCode/FLinesOfDeadCode.ql
 ql/java/ql/src/Frameworks/JavaEE/EJB/EjbContainerInterference.ql
 ql/java/ql/src/Frameworks/JavaEE/EJB/EjbFileIO.ql