added features for segmentPairEnds
common input for segPairExtractor when either sp or spe is enabled
added segmentPairEnds to segmentPairDetailsWriter
added segmentPairEnds to linear cost function and gold standard cost function
added segmentPairEnds into RandomForestCostFunction signature (only)
added segmentPairEnds to Reconstructor and SegmentationCostFunction(signature only)
added segmentPairEnds to ObjectiveGenerator
fixed syntax errors