Wasn’t 100% of the code directly written by Notch until 1-year before acquisition?

No. Jeb was the main developer from 2011 onwards, the moment Minecraft left alpha. Unless there's a time hole I'm not aware of that swallowed 2011, 2012, 2013 and most of 2014, Notch is pretty much only responsible for the very base of the game.

In addition, code is not the only thing that makes a game. Artists, music, management, and many more.

Mojang had 20+ employees way back in 2012, and they were outsourcing platform ports to other dev companies.