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3D universe refers to the titles made within the RenderWare game engine, ergo: GTA III, GTA Vice City, GTA San Andreas, GTA Liberty City Stories, GTA Vice City Stories and also Manhunt 1 and Manhunt 2. HD universe refers to the titles made within Rockstar Games' homemade RAGE engine (Rockstar Advanced Game Engine) ergo: GTA IV + Episodes of Liberty City, GTA Chinatown Wars (not made in the RAGE engine, but it's a scaled down version of GTA IV's Liberty City) and GTA V.

In Manhunt 1 theres a corrupt police officer, named Gary Schaffer, who is mentioned in a news report on one of GTA III's radio stations for having been put on trial, and cleared of his corruption charges because "the witnesses dissapeared". This happened before the events of Manhunt 1, thus placing GTA III before Manhunt 1 in the lore chronology, and confirming that Manhunt 1 belongs in the 3D universe of GTA games.

Michael De Santa mentioning Carcer City in GTA V has most likely nothing to with Manhunt 1's Carcer City, justified through Rockstar's universe logic.

3D universe lore chronology; GTA Vice City Stories (1984), GTA Vice City (1986), GTA San Andreas (1992), GTA Liberty City Stories (1998), GTA III (2001), Manhunt 1 (2003), Manhunt 2 (2007)

HD universe lore chronology: GTA IV (2008), Episodes of Liberty City (2009), GTA Chinatown Wars (2009), GTA V (2013)

Hope I'm making some sense here.