implement the new optimization method given from Shiva, also made isbonded based on the zmatrix, lastly made the cost based on errJac
Got mdminimization working, however not sure if the error that is feeded into the algorithm is in the right format
moved mdmini to MSQCApps. Did minor changes to errJac.m but changed it back to normal.
Merge branch 'master' of https://github.com/gotteric/master_MSQC into mdmini