[Core] Add flag to check if RoundTripPasses need to be run.

This would allow other flavor specific contexts to override the default value,
if they want to optionally run the round trip passes.

There is some information lost like the original file owner of the atom with
RoundTripPasses. The Gnu flavor needs this information inorder to implement
LinkerScript matching and for other diagnostic outputs such as Map files.

The flag also can be used to record information in the Atom if the information
to the Writer needs to be conveyed through References too.