Remake/reimagining of both with retcons galore. "Zero" represents the character's place in those events as well as this being the "zero" story that takes place pre-MGS1.
It all makes sense in the Kojima part of my brain.
Konami showed a brief demo of Metal Gear Solid: Ground Zeroes at their Metal Gear 25th anniversary event today. Snippets of footage showed Snake avoiding searchlights, riding a jeep, and calling a helicopter in for evacutation.