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add ConfigFlags.fillFromArgs to a number of relevant config-files

Walter Lampl requested to merge wlampl/athena:add_fillFromArgs into master

I noticed that some of the config-files with main sections did not call ConfigFlags.fillFromArgs. This is necessary to set config-flags from the command-line, like athena --CA myPackage/myConfig.py cfgFlag=value.

This MR adds this call to a number of files where this might be relevant.

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