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.
This change adds the notion of "overflow ids", which can be used
during shrinking to facilitate applying transformations that would
otherwise have become inapplicable due to earlier transformations
being removed.
