Minimize the number of places that "remake_parm" is called -- it would be best
if this is called only once... right before a topology file is printed. This
way, atoms don't get re-ordered while you're potentially working on it (unless
you do an "outparm" first).

Also make sure that when reordering molecules, atoms keep their order as best as
possible.  This *seems* to be very important to pmemd (it makes certain
assumptions about atom ordering... perhaps with regards to water atom ordering
when using SETTLE? Not sure)
Take out a remake_parm at the end of deleteBond. Also add in a bunch of
"remake_parm" calls in the test suite for add/deleteDihedral to get those tests
passing again (and reflect the way those commands have to be used).
Add "remake_parm" back to deleteBond... sigh.
Merge pull request #19 from swails/fix_reorder

Fix reorder