Task #2999: Move all logging in core library and tools to use MDLogger
Create central log handle for calls to gmx_fatal
The calls to gmx_fatal and friends currently go directly to stderr or to a legacy file for logging.
It is proposed to instead create a central logging instance in the same place that can be initialized from tools (or be default initialized the first time something is supposed to be logged).
This would allow moving to a state where all logging can go through the new logging infrastructure.