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local-submit does not read /etc/certmonger/certmonger.conf so options set there cannot override default behavior.
It gets the location of the preferences file via the environment which isn't being set so it defaults to the HOME directory which in this case is /run/certmonger/.config/certmonger/certmonger.conf
Metadata Update from @rcritten: - Issue assigned to rcritten
The problem was that certmonger was using a per-session environment and not the system environment. Re-linking will fix this.
https://pagure.io/certmonger/pull-request/193
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