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Made the output do* flags depend on the output file names

Tomasz Bold requested to merge make-doOutput-flags-depend-on-file-output-specification into master

In this MR the doWriteXYZ and XYZFileName file name flags are by default related. I.e. if the file name is nonempty then respective "do" is set to true. Tagging @rbielski as this is followup of !27215 (merged) @wlampl @emoyse

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