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
does it make sense to still have the parameter?