removed deprecated code for loading exons from pipeline.cpp; shifted the check for how many files are provided to the function which actually loads the exons; changed main pipeline code to collect up all of the exons and then output them all at the end, rather than one at a time (in preperation for adding fdr correction later). This also means we can sort them and output them in sorted order, which is now done. Regression test output files were updated to reflect this change in the order of the otuput exons