Fix issue with config autoincrements getting too large #2298
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Fix add_or_update_settings to not use upsert if the setting already exists. This was incrementing the autoincrement to much because of the autoincrement. This is because postgresql's upsert functionality works by inserting the new record and then deleting the old one which increments the autoincrement. This was causing issues when augur was being run many times in sequence.
This PR fixes #2145
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