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Q: I've added extra fields to the domains and/or records table. Will this eventually affect the resolution process in any way?
A: No, the gmysql backend uses several default queries to provide PowerDNS Server with data and all of those refer to specific field names, so as long as you don't change any of the predefined field names you are fine.
Q: Can I specify custom sql queries for the gmysql / gpgsql backend or are those hardcoded?
A: Yes you can override the default queries by specifying them as gmysql-launchname-queryname= in pdns.conf. You can find the default queries with pdns_server --launch=gmysql --config