Automatically add flags when running mqat

We would like to add a possibility to automatically set flags in PDB after we run mqat. The main inspiration for this functionality is setting the "core column issue" flag when we run mqat and know if there are core columns that had to be disabled. Up to now this flag setting was done by hand and caused some discrepancies with the data in PDB and real core column issues. A potential other use case is setting the flag for communication failure (still to be discussed). Tagging @gstark @lmeng @epianori @theim @hoide @chhultqu