The method set() does not exist on SilverStripe\Config\Coll...nfigCollectionInterface. It seems like you code against a sub-type of SilverStripe\Config\Coll...nfigCollectionInterface such as SilverStripe\Config\Coll...nfigCollectionInterface.
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Ignorable by Annotation
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If this is a false-positive, you can also ignore this issue in your code via the ignore-call annotation