Fized stoichiometry matrix initialization, added penames to reablib reactions, began work on LogicalReaction to sum the contributions of different fitting functions provided by reaclib
we need an autodiff library at some point (or we need to roll our own but I do not think that makes sense). CppAD is well tested and header only and easy to include. It is also Liscene compatible with GPL v3.0. Here we bring it in as a dependency
