remove redundant cleavage_semi
style fixes
add four new protein releated mass change options
add threading parameter
add contrast angle parameter
add total peaks parameter
add "use neutral loss window" parameter
change parameter name
change parameter name
change parameter name
style fixes
restructure the XML rewrite part, putting path settings to the beginning, indroduction fo a new boolean "tandem_params_defaults" that indicates if we use the protk default file or not
only change the XML file in cases where we do not use the standard protk tandem config file. That is only if the user provides an own config file with --tandem-params. The path variables will be set in both cases.
set the threads parameter independent of the used config file