Logging printStackTrace and err output

[Brandhoej]

In some cases System.err.println and printStackTrace is being used instead of a log function (See InProcessServer, GrpcServer and probably more).

• The printStackTrace should have a logging function which I believe should have the same urgency for all exceptions.
• The System.err.println should maybe be a fatal log.

Also we have to consider when we should use System.err.println```for ouput instead of stdio``.