The approach followed has been, wherever possible, simply modify the existing classes to allow the new approach, or where it can not be accomodated along wit hthe old approach, to simple duplicate the class and make the small number of required changes.
We wantr to continue to run the old analysis, since we will need to validate the new approach against the old, and only once we have fully, validated functionality, can we consider dropping the support for the old approach.
This code is still under heavy development - there may still be some UNUSED VARIABLES in the compilation that are there because they will be needed later. Also there are lots of commentd cout statements still needed because this is not fully functional, but we think that this needs to be merged quickly now as we need to be able to base other development on it to progress further.
As such we can't tidy it up, remove all the commented code etc, at the moment, since it is not clear what will still be needed.