You're right ... there were changes to both query_factory.php and functions_categories between zc1.3.8a and 1.3.9c. The attached zip-file has the merged version that combines Query Cache v1.6 and the respective files from ZC 1.3.9c; there is no directory structure in the zip-file, so you need to copy the files to:
/includes/classes/db/mysql/query_factory.php
/includes/functions/functions_categories.php



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