[GR-3170] Various fixes for plyr package and debugging.

.../com/oracle/truffle/r/nodes/builtin/base/BasePackage.java

...src/com/oracle/truffle/r/nodes/builtin/base/OldClass.java

.../com/oracle/truffle/r/nodes/builtin/base/UpdateClass.java

...m/oracle/truffle/r/nodes/builtin/base/UpdateOldClass.java

...e/truffle/r/nodes/builtin/compiler/R/compiler_overrides.R

.../com/oracle/truffle/r/nodes/binary/BinaryBooleanNode.java

...acle/truffle/r/nodes/control/ReplacementDispatchNode.java

...c/com/oracle/truffle/r/nodes/control/ReplacementNode.java

...acle/truffle/r/nodes/function/FunctionDefinitionNode.java

...racle/truffle/r/nodes/function/PeekLocalVariableNode.java

...com/oracle/truffle/r/nodes/function/RCallSpecialNode.java

...cle/truffle/r/nodes/instrumentation/RInstrumentation.java

...est/src/com/oracle/truffle/r/test/ExpectedTestOutput.test

...le/truffle/r/test/builtins/TestBuiltin_anyDuplicated.java

...ffle/r/test/builtins/TestBuiltin_anyDuplicatedmatrix.java

...oracle/truffle/r/test/builtins/TestBuiltin_operators.java

.../com/oracle/truffle/r/test/builtins/TestBuiltin_prod.java

...com/oracle/truffle/r/test/builtins/TestBuiltin_sinpi.java

...cle/truffle/r/test/library/base/TestSimpleAssignment.java