Summary: The order of the sentences do not matter.
The sentences in the baseline_result, input sentences and the ground truth extractions are not in order. They are not required to be in order. The results file has id of the sentence in the order in which they are read by the reader. The
run.py already takes care of formatting your extractions to the correct format to be written to the results file. Again, here the ids are only generated in the results file and they are not unique ids.