Logging printStackTrace and err output

In some cases ``System.err.println`` and ``printStackTrace`` is being used instead of a log function (See [InProcessServer](https://github.com/Ecdar/j-Ecdar/blob/d1d1feaad68fbe73026d35d2fc70cb770f5f5c53/test/connection/InProcessServer.java#L32), [GrpcServer](https://github.com/Ecdar/j-Ecdar/blob/9d53d7a104cab5067b7337fa6967e84e6d9d8e7a/src/connection/GrpcServer.java#L48) 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``.

Start by inspecting test/connection/InProcessServer.java at line 32 and src/connection/GrpcServer.java at line 48, then search for other uses of System.err.println and printStackTrace. Review the project's existing log functions and decide how exception urgency and stderr versus standard output should be handled; done means the direct output uses the agreed logging approach consistently.

Written by the indexing model from the issue text.