FeatureFinderMultiplex

The FeatureFinderMultiplex TOPP tool can detect peptide features in MS1 data. It is particularly suited for the analysis of labelled experiments, such as SILAC or Dimethyl labelling. The main algorithm was previously submitted in pull requests #868 and #889. - This pull requests contains the user interface, calculation of the fold changes and the export to the final data formats: consensusXML, featureXML and mzQuantML. 
I refactored, see generateKnockoutMassShifts(). IMO, a separate class would probably not be used anywhere else.