The def-use manager was being incorrectly updated in
TransformationPermutePhiOperands, and this was causing future
transformations to go wrong during fuzzing. This change updates the
def-use manager in a correct manner, and adds a test exposing the
previous bug.
Fixes#4300.
Adds a virtual method, GetFreshIds(), to Transformation. Every
transformation uses this to indicate which ids in its protobuf message
are fresh ids. This means that when replaying a sequence of
transformations the replayer can obtain a smallest id that is not in
use by the module already and that will not be used by any
transformation by necessity. Ids greater than or equal to this id
can be used as overflow ids.
Fixes#3851.
