AccurateMassSearchEngine annotation of input map (not only mzTab output)

Sometimes we want to continue to work with featureXML/consensusXML instead of mzTab.
This PR allows to annotate the input maps of AMSE with the results and write them back to disk.

plus:
cleanup of related code (const, duplicated code, inefficient code...)
some more documentation
here, no, but cleaning this up is a bigger operation.
The whole concept of MassTrace is very confusing because it can operate on raw and smoothed data (which you have to generate first). Properties like FWHM are then computed on one of both, but when asking myMassTrace.getFWHM() you better know which one it was...
So I propose to remove smoothed intensities entirely from a mass trace. Instead, use a new vector of MT's which contains the smoothed intensties. This also cleans up lots of if-else within the MT code. But that's another pull request for the future...