Decouple t_inputrec from MDModules

Decouple t_inputrec from MDModules

t_inputrec no longer depends on IInputRecExtension fields being
initialized, so it is not necessary to initialize it in gmx::MDModules.
Now t_inputrec can again be initialized without gmx::MDModules,
clarifying responsibilities.

For now, this again removes the need to use gmx::MDModules for just
reading t_inputrec.  These locations may need further changes as
responsibilities move around more, but in any case, t_inputrec ownership
should be better somewhere else than in MDModules.

Add constructor and destructor to t_inputrec to make it easier to manage
its instances.  Disallow copying (since that is tricky to implement
correctly), and do a manual only-what-is-required copy in PME
reinitialization, which is the only place that relied on copying

Change-Id: I52e0a17b13a0b7dad886fdf1b7d09bcbfcf961aa