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.
TransformationContext now holds a std::unique_ptr to a FactManager,
rather than a plain pointer. This makes it easier for clients of
TransformationContext to work with heap-allocated instances of
TransformationContext, which is needed in some upcoming work.
