The clock is hidden from the players and the crowd.

Answers to your questions:

1. The referee.
2. On the fly.
3. The referee decides.
4. A few moments before the end of the half.
5. Yes.
6. Football is a fluid game that doesn't have the stop-start nature of things like American "Football" or Ice Hockey. The game doesn't have set plays like Rugby For Retards, and even set pieces can be improvised - being awarded a free kick only means that you have the *right* to take a free kick from a dead ball - it doesn't necessarily mean you /have/ to. The only time the ball is truly dead is when it goes out of play.

The rest of the world isn't obsessed by having the ability to play its games in 3-second bursts. What is the objective difference between stopping the clock, and adding the time on at the end?

Remember, the game played in the World Cup Final doesn't substantially differ from that played in the barrios of Sao Paulo in terms of equipment - there's a pitch, a ball, and two goals.