[core.smf] replacing some System.err.println with logging commands OXAL-493
[core.smf] replacing some System.err.println with logging commands
OXAL-493

EuropeanSpallationSource/openxal,EuropeanSpallationSource/openxal,EuropeanSpallationSource/openxal,EuropeanSpallationSource/openxal,EuropeanSpallationSource/openxal