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Just set JAVA_OPTS before running run.bat
I was considering modifying the run.bat so as to parse the run.conf rather than setting the JAVA_OPTS before running the run.bat.
My solution was to include :
REM setting JAVA_OPTS to : set JAVA_OPTS=%JAVA_OPTS% -Duser.timezone=Europe/Bucharest
into the run.bat before the first line that sets JAVA_OPTS, but I consider that to be rather unpleasant :P.
I thought there was some kind of OS independent configuration file for this.