ClickCookieOnly.js

CookieBot = {
  start: function() {
  	this.clickInterval = setInterval(function(){
			// Click the large cook as fast as possible!
			$("#bigCookie").click();
		}, 1);

	this.goldenCookieInterval = setInterval(function() {
		Game.goldenCookie.delay = 0;
	});
	
	this.buyInterval = setInterval(function(){
		// Sometimes a golden cookie will appear to give you a bonus
		// Click that too!
		$("#goldenCookie").click();
		}, 1000);
	},
	stop: function() {
		clearInterval(this.goldenCookieInterval);
		clearInterval(this.clickInterval);
		clearInterval(this.buyInterval);
	}
};

CookieBotMod.js

CookieBot = {
  start: function() {
		this.clickInterval = setInterval(function(){
			// Click the large cook as fast as possible!
			$("#bigCookie").click();
		}, 1);
		this.buyInterval = setInterval(function(){
			// Sometimes a golden cookie will appear to give you a bonus
			// Click that too!
			$("#goldenCookie").click();

			// Now we need to buy stuff with our money.
			// Start by trying to buy the most-expensive item
			var last = [].slice.call($$(".product.enabled")).reverse()[0];
			if (last) {
				last.click();
			} else {
				// Then try to buy the most expensive upgrade
				var upgrade = [].slice.call($$(".upgrade.enabled")).reverse()[0];
				if (upgrade && !(/\[85\]/.test(upgrade.onclick.toString()))) {
					upgrade.click();
				}
			}
		}, 1000);
	},
	stop: function() {
		clearInterval(this.clickInterval);
		clearInterval(this.buyInterval);
	}
};