Additional improvements to Json IO

[PDoakORNL]

With regards to the life cycle of the object, RAII could be better.
If we're going to throw for a bad file and the purpose of close file is it to prepare for another open...
It seems be better to just have the file as a constructor argument and do no "reseting" closing the file in the destructor.

With regards to repeated tags, that seems like invalid input and an exception should be thrown.