Maybe its time for you start implementing a whole development workflow using such tools as yeoman http://yeoman.io/. This will help control all your dependencies, build process and if you wanted, automated testing. Its a lot of work to start with but once implemented will make future changes a lot easier.

I suggest that you use something like Backbone. Backbone is a RESTFUL supported javascript library. Ik makes your code cleaner and more readable and is powerful when used together with requirejs.

http://backbonejs.org/

http://requirejs.org/

Backbone isn't a real library. It is meant to give structure to your javascript code. It is able to include other libraries like jquery, jquery-ui, google-maps etc. Backbone is in my opinion the closest javascript approach to Object Oriented and Model View Controller structures.

Also regarding your workflow.. If you build your applications in PHP use the Laravel library. It'll work flawlessly with Backbone when used with the RESTfull principle. Below the link to Laravel Framework and a tutorial about building RESTfull APIs:

http://maxoffsky.com/code-blog/building-restful-api-in-laravel-start-here/

http://laravel.com/

Below is a tutorial from nettuts. Nettuts has a lot of High Quality tutorials:

http://net.tutsplus.com/tutorials/javascript-ajax/understanding-backbone-js-and-the-server/

I'll go over some simple things that may, or may not, help you. Some might be obvious, some might be extremely arcane.

Step 1: Compartmentalize your code

Separating your code into multiple, modular units is a very good first step. Round up what works "together" and put them in their own little encased unit. don't worry about the format for now, keep it inline. The structure is a later point.

So, suppose you have a page like this:

It would make sense to compartmentalize so that all the header-related event handlers/binders are in there, for ease of maintenance (and not having to sift through 1000 lines).

You can then use a tool such as Grunt to re-build your JS back to a single unit.

Step 1a: Dependency management

Use a library such as RequireJS or CommonJS to implement something called AMD. Asynchronous Module Loading allows you to explicitely state what your code depends on, which then allows you to offload the library-calling to the code. You can just literally say "This needs jQuery" and the AMD will load it, and execute your code when jQuery is available.

This also has a hidden gem: the library loading will be done the second the DOM is ready, not before. This no longer halts load-up of your page!

Step 2: Modularize

See the wireframe? I have two ad units. They'll most likely have shared event listeners.

Your task in this step is to identify the points of repetition in your code and to try to synthesise all this into modules. Modules, right now, will encompass everything. We'll split stuff as we go along.

The whole idea of this step is to go from step 1 and delete all the copy-pastas, to replace them with units that are loosely coupled. So, instead of having:

ad_unit1.js

 $("#au1").click(function() { ... });

ad_unit2.js

 $("#au2").click(function() { ... });

I will have:

ad_unit.js:

 var AdUnit = function(elem) {
this.element = elem || new jQuery();
}
AdUnit.prototype.bindEvents = function() {
... Events go here
}

page.js:

 var AUs = new AdUnit($("#au1,#au2"));
AUs.bindEvents();

Which allows you to compartmentalize between your events and your markup in addition to getting rid of repetition. This is a pretty decent step and we'll extend this further later on.

Step 3: Pick a framework!

If you'd like to modularize and reduce repetitions even further, there are a bunch of awesome frameworks around that implement MVC (Model - View - Controller) approaches. My favourite is Backbone/Spine, however, there's also Angular, Yii, ... The list goes on.

A Model represents your data.

A View represents your mark-up and all the events associated to it

A Controller represents your business logic - in other words, the controller tells the page what views to load and what models to use.

This will be a significant learning step, but the prize is worth it: it favours clean, modular code over spaghetti.

There are plenty of other things you can do, those are just guidelines and ideas.

Code-specific changes

Here are some specific improvements to your code:

 $('.new_layer').click(function(){


dialog("Create new layer","Enter your layer name","_input", {


'OK' : function(){


var reply = $('.dialog_input').val();


if( reply != null && reply != "" ){


var name = "ln_"+reply.split(' ').join('_');
var parent = "";


if(selected_folder != "" ){
parent = selected_folder+" .content";
}


$R.find(".layer").clone()
.addClass(name).html(reply)
.appendTo("#layer_groups "+parent);


$R.find(".layers_group").clone()
.addClass(name).appendTo('#canvas '+selected_folder);


}


}


});
});

This is better written as:

$("body").on("click",".new_layer", function() {
dialog("Create new layer", "Enter your layer name", "_input", {
OK: function() {
// There must be a way to get the input from here using this, if it is a standard library. If you wrote your own, make the value retrievable using something other than a class selector (horrible performance + scoping +multiple instance issues)


// This is where the view comes into play. Instead of cloning, bind the rendering into a JS prototype, and instantiate it. It means that you only have to modify stuff in one place, you don't risk cloning events with it, and you can test your Layer stand-alone
var newLayer = new Layer();
newLayer
.setName(name)
.bindToGroup(parent);
}
});
});

Earlier in your code:

window.Layer = function() {
this.instance = $("<div>");
// Markup generated here
};
window.Layer.prototype = {
setName: function(newName) {
},
bindToGroup: function(parentNode) {
}
}

Suddenly, you have a way to create a standard layer from anywhere in your code without copy pasting. You're doing this in five different places. I've just saved you five copy-pastes.

One more:

// Ruleset wrapper for actions

var PageElements = function(ruleSet) {
ruleSet = ruleSet || [];
this.rules = [];
for (var i = 0; i < ruleSet.length; i++) {
if (ruleSet[i].target && ruleSet[i].action) {
this.rules.push(ruleSet[i]);
}
}
}
PageElements.prototype.run = function(elem) {
for (var i = 0; i < this.rules.length; i++) {
this.rules[i].action.apply(elem.find(this.rules.target));
}
}


var GlobalRules = new PageElements([
{
"target": ".draggable",
"action": function() { this.draggable({
cancel: "div#scrolling, .content",
containment: "document"
});
}
},
{
"target" :".resizable",
"action": function() {
this.resizable({
handles: "all",
zIndex: 0,
containment: "document"
});
}
}


]);


GlobalRules.run($("body"));


// If you need to add elements later on, you can just call GlobalRules.run(yourNewElement);

This is a very potent way to register rules if you have events that are not standard, or creation events. This is also seriously kick-ass when combined with a pub/sub notification system and when bound to an event you fire whenever you create elements. Fire'n'forget modular event binding!

I would suggest:

1. publisher/subscriber pattern for event management.
2. object orientation
3. namespacing

In your case Jessica, divide the interface into pages or screens. Pages or screens can be objects and extended from some parent classes. Manage the interactions among pages with a PageManager class.

For your question and comments I'll assume you are not willing to port your code to a framework like Backbone, or use a loader library like Require. You just want a better way to orgainze the code that you already have, in the simplest way possible.

I understand it is annoying to scroll through 2000+ lines of code to find the section that you want to work on. The solution is to split your code in different files, one for each functionality. For example sidebar.js, canvas.js etc. Then you can join them together for production using Grunt, together with Usemin you can have something like this:

In your html:

<!-- build:js scripts/app.js -->
<script src="scripts/sidebar.js"></script>
<script src="scripts/canvas.js"></script>
<!-- endbuild -->

In your Gruntfile:

useminPrepare: {
html: 'app/index.html',
options: {
dest: 'dist'
}
},
usemin: {
html: ['dist/{,*/}*.html'],
css: ['dist/styles/{,*/}*.css'],
options: {
dirs: ['dist']
}
}

If you want to use Yeoman it will give you a boilerplate code for all this.

Then for each file itself, you need to make sure you follow best practices and that all the code and variables are all in that file, and don't depend on other files. This doesn't mean you can't call functions of one file from other, the point is to have variables and functions encapsulated. Something similar to namespacing. I'll assume you don't want to port all your code to be Object Oriented, but if you don't mind refactoring a bit, I'd recommend to add something equivalent with what is called a Module pattern. It looks something like this:

sidebar.js

var Sidebar = (function(){
// functions and vars here are private
var init = function(){
$("#sidebar #sortable").sortable({
forceHelperSize: true,
forcePlaceholderSize: true,
revert: true,
revert: 150,
placeholder: "highlight panel",
axis: "y",
tolerance: "pointer",
cancel: ".content"
}).disableSelection();
}
return {
// here your can put your "public" functions
init : init
}
})();

Then you can load this bit of code like this:

$(document).ready(function(){
Sidebar.init();
...

This will allow you to have a much more maintainable code without having to rewrite your code too much.

Here is a simple way to split your current codebase into multiple files, using require.js. I will show you how to split your code into two files. Adding more files will be straightforward after that.

Step 1) At the top of your code, create an App object (or whatever name you prefer, like MyGame):

var App = {}

Step 2) Convert all of your top-level variables and functions to belong to the App object.

Instead of:

var selected_layer = "";

You want:

App.selected_layer = "";

Instead of:

function getModified(){
...
}

You want:

App.getModified = function() {


}

Note that at this point your code will not work until you finish the next step.

Step 3) Convert all global variable and function references to go through App.

Change stuff like:

selected_layer = "."+classes[1];

to:

App.selected_layer = "."+classes[1];

and:

getModified()

to:

App.GetModified()

Step 4) Test Your code at this stage -- it should all work. You will probably get a few errors at first because you missed something, so fix those before moving on.

Step 5) Set up requirejs. I assume you have a web page, served from a web server, whose code is in:

www/page.html

and jquery in

www/js/jquery.js

If these paths are not exactly like this the below will not work and you'll have to modify the paths.

Download requirejs and put require.js in your www/js directory.

in your page.html, delete all script tags and insert a script tag like:

<script data-main="js/main" src="js/require.js"></script>

create www/js/main.js with content:

require.config({
"shim": {
'jquery': { exports: '$' }
}
})


require(['jquery', 'app']);

then put all the code you just fixed up in Steps 1-3 (whose only global variable should be App) in:

www/js/app.js

At the very top of that file, put:

require(['jquery'], function($) {

At the bottom put:

})

Then load page.html in your browser. Your app should work!

Step 6) Create another file

Here is where your work pays off, you can do this over and over.

Pull out some code from www/js/app.js that references $ and App.

e.g.

$('a').click(function() { App.foo() }

Put it in www/js/foo.js

At the very top of that file, put:

require(['jquery', 'app'], function($, App) {

At the bottom put:

})

Then change the last line of www/js/main.js to:

require(['jquery', 'app', 'foo']);

That's it! Do this every time you want to put code in its own file!

Use javascript MVC Framework in order to organize the javascript code in a standard way.

Best JavaScript MVC frameworks available are:

• Backbone
• Angular
• CanJS
• Ember
• ReactJS

Selecting a JavaScript MVC framework required so many factors to consider. Read the following comparison article that will help you to select best framework based on the factors important for your project: http://sporto.github.io/blog/2013/04/12/comparison-angular-backbone-can-ember/

You can also use RequireJS with the framework to support Asynchrounous js file & module loading.
Look the below to get started on JS Module loading:
http://www.sitepoint.com/understanding-requirejs-for-effective-javascript-module-loading/

Categorize your code. This method is helping me a lot and does work with any js framework:

(function(){//HEADER: menu
//your code for your header
})();
(function(){//HEADER: location bar
//your code for your location
})();
(function(){//FOOTER
//your code for your footer
})();
(function(){//PANEL: interactive links. e.g:
var crr = null;
$('::section.panel a').addEvent('click', function(E){
if ( crr) {
crr.hide();
}
crr = this.show();
});
})();

In your preferred editor (the best is Komodo Edit) you may fold in by collapsing all entries and you will see only the titles:

(function(){//HEADER: menu_____________________________________
(function(){//HEADER: location bar_____________________________
(function(){//FOOTER___________________________________________
(function(){//PANEL: interactive links. e.g:___________________