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config: prefer configuration specified files
Suricata-Update was preferring the existence of "disable.conf" in $sysconfdir over it be specified in the update.yaml. Refactor the auto-conf to only search and apply the default $sysconfdir files if they don't already exist in the config. Additonally, now that the default, if not set or found will be none, log a warning if a specific configuration file is not found instead of silently ignoring. Ticket: #6172
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