[~Cory~]

----Edit------
John beat me too it

The post above is correct.

For future reference you may want to look into handling exceptions in Java. This article in the Java documentation explains exceptions pretty well:http://docs.oracle.com/javase/tutori...efinition.html
---------------
This is your problem:

[cRIO] Uncaught exception in Thread.run():
[cRIO] on thread edu.wpi.first.wpilibj.templates.RobotTemplate - main
[cRIO] edu.wpi.first.wpilibj.util.AllocationException: PWM channel 1 on module 1 is already allocated

Take a look in here:

Joystick leftStick = new Joystick(1);
Joystick rightStick = new Joystick(2);
Joystick thirdStick = new Joystick(3);
Jaguar leftdrive = new Jaguar(1);
Jaguar rightdrive = new Jaguar(2);
Button shooter1 = new JoystickButton(thirdStick,3);
Button shooter2 = new JoystickButton(thirdStick,4);
Button shooter3 = new JoystickButton(thirdStick,5);
Button shooterStop = new JoystickButton(thirdStick,2);
Jaguar shooter = new Jaguar(3);
RobotDrive drive = new RobotDrive(1, 2);

and

drive = new RobotDrive(leftdrive,rightdrive);