refactor: switch metabolite and reaction identifiers to BiGG style

[edkerk]

Current metabolite IDs are a mixture of yeast-GEM derived (s_0001) and default IDs as suggested by RAVEN (m0001). Reaction IDs are a custom format (y_000001). Change all of this to BiGG-style IDs, which simplifies checking of reactions by just the metabolite IDs, allow easy integration with Escher, etc.
This would break older scripts so is for now scheduled as a major release. A table with old and new IDs will be retained.