Refactor align_against_collection(), streamlined handling of "reverse" positions

There was code handling conversion to "reverse" positions in several places in dynprog.cpp, segment.cpp, and vdj_assign.cpp, with at least one pair of back-and-forth conversions. Now all these operations are removed and replaced by a unique AlignBox::reverse() call in align_against_collection(). This function is also refactored.