Support concurrent t_topology and gmx_mtop_t use

Support concurrent t_topology and gmx_mtop_t use

Make gmx_mtop_t_to_t_topology() take a boolean flag that specifies
whether to free memory from mtop or not.  This makes it possible to
convert an mtop to a t_topology and then use both in subsequent code.
This in turn makes a piecewise conversion from t_topology to gmx_mtop_t
possible.

Using these two concurrently currently always leads to memory leaks, but
these should mostly be temporary during the conversion, and can be
sorted out separately if necessary.

Part of #1862.

Change-Id: Iccd6039c2226d1dc617963878e5640bb53f09ad6