refs #6449 started enabling MDBoxSaveable class

as class which saves to NeXus
refs #6449 Extracted NexusIO from box controller

and enabled number of other small things related to file-based boxes
refs #6449 Enabled main part of MDBoxFlatTree (except file based)

Temporary Reverted box controller to with control of boxes to change to vanilla box controller and disabling BC copy constructor, as it is too complex for file based workspaces.