The following contains MAJOR SPOILERS for the “First Contact” episode of the SciFi Channel’s “Stargate: Atlantis.” It’s always big news when a member of “Stargate SG-1″ visits “Atlantis,” and this week the “Save Daniel Jackson” fans were in heaven when Michael Shanks guest-starred. This episode was obviously intended to be the “mid-season finale” or whatever they call it when SciFi Channel chops a season in half, something that frustrates me no end. However, with the network’s decision to run the program’s final year almost in one piece, we only have to wait two weeks. Next Friday will be the two-hour premiere of “Sanctuary.” What happened this week was that Daniel Jackson arrives at the city to follow up on a lead on a secret laboratory an Ancient scientist named Janus (from …