ParserTests are the only place where we still run the parser in "no tidy" mode. We need to update the output of the parserTests used by the Cite extension to have properly tidied output. Adding !! version 2 as the first line of your parserTests file opts in to this new behavior, and you can easily see which tests fail. Usually the clean up is pretty straightforward.
See https://gerrit.wikimedia.org/r/565146 for a description of typical fixups.
See https://gerrit.wikimedia.org/r/568093 patchset 1 for how to get started (just add !! version 2 to all your parser tests files and see what breaks!