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. 
thats a pretty long 230 lines function. would it make sense to move this into the OpenMS lib, is this generic/re-useable enough? If not could it at least live as an extra class outside the `FeatureFinderMultiplex` class?