Use C++ replacement for md_logging.*

Use C++ replacement for md_logging.*

Replace md_logging.h with the new C++ implementation.  This removes the
need to pass around a (FILE *, t_commrec *) tuple for just calling
md_logging.h routines.  Initialize the logger in runner.cpp to get the
same output as earlier.  For now, output is the same as earlier, but the
new interface could also relatively easily support, e.g., automatic line
wrapping.

Further changes should see all of fplog access go through the same
object (possibly after finetuning the interface), but that would be too
large of a change to do in one go.

Thread affinity tests for now just discard the log output, making them
more silent.  Future changes should see the log output verified, to
check that the correct messages are produced.

Related to #1505, closes #1644.

Change-Id: I0895b752b040d231cacb49a3a7a48d26c6096944