The Grid class has some slightly better hacks to handle roundoff error
with computing the upper bounds.
I had to revert this patch because the nonbonded list unit tests failed
after I applied it. And it wouldn't compile without modification -
perhaps a missed change to the corresponding header?
And the main event. I added a class internal::ObjectPointer which can be
used to (guess what?) store pointers to Objects.
This one wouldn't compile - I think you missed the changes to Object.h.
And there seemed to be a lot of extraneous junk in there too which I
took out, which looks like you'd put in for temporary debugging -
changes to the build system, disabling a bunch of unit tests, etc.