TruckU on Speed Channel did an episode on this awhile back. They added a cold air intake, along with a cat back exhaust system. The PCM (power control module) box will "learn" the improvements, and no, the system will not run lean.
They (TruckU) said that if you were too impatient for the system to learn the new setup, disconnect the negative battery cable; wait about 5 minutes, and re-connect. This clears the PCM, and forces it to relearn upon startup and a 10 minute drive.
The myths continue....sigh.