made some changes to the SPOT algorithm

added ecoli-core matrix from min's matlab script

added optimized flux values as starting point for debugging purposes
Debugging...

changed ModelFormatter for fixed biomass when optimizing SPOT

added code in abstract IpoptSolver class for debugging purposes
made some optimizations/clarity to Objective function
more debugging
Yeast 7.11 added to Model Collection, ...

models written in SBML invalid level 3 format rewritten as level 2.