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I think that this issue was resolved in #181 and the setting is now commented. Could you test the current behaviour?
Including those files shadows the configuration managed by this formula, which is why it should be removed / commented. Adapting the configuration patterns for MariaDB would require a more fine grained approach to the distribution of settings in the default my.cnf and files in /etc/mysql/mariadb.conf.d/.
When using the formula on a debian stretch. In the diff on my.cnf I get :
I think this should be kept.
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