fix .plotCxDiff
Remove old cx filter methods and replace them by new ones

- Removes filterMatchedEMRTsByCommonPeaks, plotCrossMatchingSummary,
  plotCrossMatchingDiff, plotCrossMatchingCumulativeNumberOfFragments.
- Changes plotCrossMatchingPerformance (replaces old plot functions by a simple
  two panel plot).
- Adds filterUniqueMatches and filterNonUniqueMatches (replaces
  filterMatchedEMRTsByCommonPeaks).