ObjectCloner - make deep copies, ID to Abbrev

MetaboliteUsedMap and invalidReactions list need to be deep copied so
that if there are optimizations and the original database is modified,
the optimization retains the properties it had when created, such as if
a metabolite changes used status in the original file, it will retain
its original used status in the optimization.
Still have to implement this functionality.
Also changed Metabolite ID column header to Metabolite Abbreviation, and
same change for reactions.