Moving old Setup xml stuff into legacy namespace

Making room for the new stuff.
WIP Fixing setupFileCreator with new format
Some more comments and extra help at exception.
New SetupXMLReader implemented
Adding tests for the new setup reader

I just copied the tests for the legacy reader and made sure that if it
contained the same informtation, the reader would return the same info,
and that seems to be working.
Add test for reader switching
Switch SetupXMLReader by looking for <runfolder>

If this tag is present it will be assumed that this is a file on the
legacy format.
Update the README with new input format