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Hmmmm... possible spoilers here... navigate with care.
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In the FAQ @ IMDb.com

Does this movie belong to Alien franchise?

The film started out as a prequel to the original Alien film.

Some recent history: there had been talks of a fifth Alien movie for years, with alternating contributions from James Cameron and Ridley Scott. In fact, Scott had committed to an Alien sequel or prequel about ten years ago, but aborted the project when the studio opted to make the AvP movies first, and Scott was no supporter of the Alien/Predator crossover franchise. After the disappointing box office from Aliens vs Predator: Requiem, the studio shelved the AvP franchise again to go back to the original plan.

The prequel film was supposed to cover the origins of the Weyland-Yutani Company. However, a full agreement could not be reached; Scott envisioned an explicitly R-rated movie, but since this would limit the target audience, the studio demanded a drastically reduced budget to which Scott wouldn't agree. So the Alien prequel film was abandoned in favour of an original project called Prometheus. Some ideas for the aborted Alien prequel would be used, and the story would contain elements reminiscent of the Alien backstory, but it would be a movie separate from the Alien Universe.

In an interview, however, Michael Fassbender confirmed that this is actually an Alien movie, taking place in the Alien universe. ‘Prometheus’ Is Absolutely Connected To ‘Alien,’ Says Michael Fassbender. Ridley Scott was quick to retort, stating that "this is not an Alien prequel"; it does appear that Scott intends to make Prometheus completely different from the other Alien films. Exactly how is not yet clear, but it is likely that the story takes place within the same universe, but it is not directly connected to the events of the original.

There may of course be some misdirection on part of the film makers to help highten interest in the film.

According to Skymovies.com, there is a rumor that they are building a Space Jockey set, but no confirmation has been made yet. Recently leaked photos from the set of the film heavily suggest the movie is an Alien film. The set designs are very much inspired by if not designed and built by H.R. Giger. Like Nectar From The Gods! Leaked 'Prometheus' Images! - Moviepilot.com

The most recent trailer for Prometheus shows footage of the Derelict Spacecraft and "Space Jockey" creatures from the first Alien film, proving that indeed the film does take place in the same fictional universe as the previous Alien films.Prometheus - Official Trailer [TRUE HD] - YouTube

Regarding the "xenomorph", Ridley Scott stated in an interview that it will not appear in the movie:

"No. Absolutely not. They squeezed it dry. "

And regarding the link to the first movie.:

"EGE: So you are linking this directly with the Alien films?

RS: Not at all.

EGE: Not at all?

RS: No.

EGE: No?

RS: I mean, you could actually say, and theres a quote I did, a pretty good quote: By the end of the third act you start to realize theres a DNA of the very first alien, but none of the subsequent aliens. To tell you what that is is a pity, and Im not going to tell you, because its actually pretty good, pretty organic to the process and to the original. But we go back, we dont go forward."

In the same interview, Scott confirms that H.R. Giger is doing "a little bit" of design work on the project. Interview: Ridley Scott Talks Prometheus, Giger, Beginning of Man and Original Alien | Filmophilia

Prometheus (2012) - FAQ