Replace gmx::Mutex with std::mutex

Replace gmx::Mutex with std::mutex

We use no mutexes during the MD loop, so performance is not a serious
consideration and we should simplify by using std components.
Eliminated components of thread-MPI that are now unused.

In particular, this reduces the cross-dependencies between the
libgromacs and threadMPI libraries.

Minor style improvements around set_over_alloc_dd.

Part of #3892