The malicious code is not on the source itself, it’s on tests and other files. The building process hijacks the code and inserts the malicious content, while the code itself is clean, So the co-manteiner was able to keep it hidden in plain sight.
So it’s not that the Volkswagen cheated on the emissions test. It’s that running the emissions test (as part of the building process) MODIFIED the car ITSELF to guzzle gas after the fact. We’re talking Transformers level of self modification. Manchurian Candidate sleeper agent levels of subterfuge.