Move all logging in core library and tools to use MDLogger
Currently, logging is still not done in a consistent way in the core GROMACS library.
While large parts of the code in the actual mdrunner have been moved to use it, other parts are still printing directly to stderr or stdout.
This is an umbrella task that should be used to organize subtasks that are focusing on individual parts of the code.
Extend MDLogger levels
Added logging levels for errors and debug information.
Extended tests to check those.