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libbeat cmds do not respect instance.Settings #10720

@simitt

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@simitt

Several commands in libbeat/cmd do not respect instance.Settings, but only use dedicated attributes from it. This can lead to bugs for e.g. running export template etc.
The bug was originally found in elastic/apm-server#1922.

Ensure that the settings are passed on to all cmds and remove deprecated Init() .

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