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cli: Consistent set up of logging infrastructure for subcommands

Patrick Steinhardt requested to merge pks-log-subcommands-consistent-configuration into master

This MR changes our subcommands to consistently set up the logging infrastructure.

Closes Praefect metdata subcommand output is no longer... (#5479 - closed).

Closes praefect check command output have gRPC verbose... (#5509 - closed).

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