[MSGFPlusAdapter extension]

- added input parameters for the search
- replaced the static parameter values with the input parameter values
- write the idXML based on the tsv file
  - added search parameters
  - add protein_identifications
  - parse the input mzML File to get the RT information in the idXML file
- extended IDPosteriorErrorProbability with MSGF+ search engine

modified:   ../src/topp/IDPosteriorErrorProbability.cpp
modified:   ../src/topp/MSGFPlusAdapter.cpp
deleted:    ../src/topp/MSGFplusAdapter.C