Remove pbcutil <-> mdtypes cyclic dependency

Remove pbcutil <-> mdtypes cyclic dependency

This may not be the cleanest solution, but it separates the
responsibilities of having knowledge of t_state and t_inputrec from
the low-level code of preserving the box shape.  For a cleaner solution,
do_box_rel() could be separated into separate init and perform
functions, and having an internal data structure so that only the init
function would need parameters like the dimensions to correct.
Other alternative would be to move also do_box_rel() into state.cpp, but
not sure if there was a deeper reason putting it in pbcutil in the first
place.

Part of #1854.

Change-Id: I7ae16d3c2e795bd08d28da6111debf5d9d17599e