Remove references of third-party libraries on cilantro object

This is to improve clarity of the code as well as make it possible
to load the individual third-party modules for use in the project or
override the core libraries if existing in a project.

The dropped references include:

- `c.$`
- `c._`
- `c.Backbone`
- `c.Marionette`
- `c.Highcharts`

These dependencies must now be included explicitly in the dependencies
array for the module.

In addition, the subscribe/publish hooks for Marionette.ItemView have
been removed. There were only two areas this was being used and they
were simply replaced with `c.mediator`.

spec/ControlSpec.js

@@ -1,5 +1,5 @@
-define(['cilantro', 'text!/mock/fields.json'], function (c, fieldsJSON) {
-    var fields = new c.Backbone.Collection(JSON.parse(fieldsJSON));
+define(['backbone', 'cilantro', 'text!/mock/fields.json'], function (Backbone, c, fieldsJSON) {
+    var fields = new Backbone.Collection(JSON.parse(fieldsJSON));
 
     describe('FieldControl', function() {
         var control;

spec/RouterSpec.js

@@ -1,4 +1,4 @@
-define(['cilantro'], function(c) {
+define(['jquery', 'underscore', 'backbone', 'cilantro'], function($, _, Backbone, c) {
 
     var routes;
 
@@ -8,7 +8,7 @@ define(['cilantro'], function(c) {
             routes = [{
                 id: 1,
                 route: 'foo/',
-                view: new c.Backbone.View,
+                view: new Backbone.View,
                 el: '#region1'
             }, {
                 id: 2,
@@ -18,7 +18,7 @@ define(['cilantro'], function(c) {
             }, {
                 id: 3,
                 route: 'foo/',
-                view: new c.Backbone.View,
+                view: new Backbone.View,
                 el: '#region3'
             }, {
                 id: 4,
@@ -27,24 +27,24 @@ define(['cilantro'], function(c) {
                 el: '#region3'
             }];
 
-            c.$('#region1, #region2, #region3').remove();
+            $('#region1, #region2, #region3').remove();
 
-            c.$('body')
+            $('body')
                 .append('<div id=region1 />')
                 .append('<div id=region2 />')
                 .append('<div id=region3 />');
 
             c.router.options.el = 'body';
             c.router.register(routes);
-            c.Backbone.history.start({pushState: false, hashChange: true});
+            Backbone.history.start({pushState: false, hashChange: true});
         });
 
         afterEach(function() {
-            c.Backbone.history.navigate();
-            c.Backbone.history.stop();
-            c.Backbone.history.handlers = [];
+            Backbone.history.navigate();
+            Backbone.history.stop();
+            Backbone.history.handlers = [];
 
-            c._.each(c._.keys(c.router._registered), function(id) {
+            _.each(_.keys(c.router._registered), function(id) {
                 c.router.unregister(id);
             });
             c.router._handlers = {};
@@ -53,21 +53,21 @@ define(['cilantro'], function(c) {
         describe('Register', function() {
 
             it('should register', function() {
-                expect(c._.keys(c.router._registered).length).toEqual(4);
+                expect(_.keys(c.router._registered).length).toEqual(4);
                 expect(c.router._loaded.length).toEqual(0);
-                expect(c._.keys(c.router._handlers).length).toEqual(2);
-                expect(c._.keys(c.router._routes).length).toEqual(2);
+                expect(_.keys(c.router._handlers).length).toEqual(2);
+                expect(_.keys(c.router._routes).length).toEqual(2);
             });
 
             it('should load non-route routes on register', function() {
                 c.router.register({
                     id: 5,
                     view: new Backbone.View
                 });
-                expect(c._.keys(c.router._registered).length).toEqual(5);
+                expect(_.keys(c.router._registered).length).toEqual(5);
                 expect(c.router._loaded.length).toEqual(1);
-                expect(c._.keys(c.router._handlers).length).toEqual(2);
-                expect(c._.keys(c.router._routes).length).toEqual(2);
+                expect(_.keys(c.router._handlers).length).toEqual(2);
+                expect(_.keys(c.router._routes).length).toEqual(2);
             });
         });
 
@@ -76,7 +76,7 @@ define(['cilantro'], function(c) {
             it('should unregister', function() {
                 c.router.unregister(routes[0].id);
 
-                expect(c._.keys(c.router._registered).length).toEqual(3);
+                expect(_.keys(c.router._registered).length).toEqual(3);
                 expect(c.router._loaded.length).toEqual(0);
             });
 
@@ -86,12 +86,12 @@ define(['cilantro'], function(c) {
                     view: new Backbone.View
                 });
 
-                expect(c._.keys(c.router._registered).length).toEqual(5);
+                expect(_.keys(c.router._registered).length).toEqual(5);
                 expect(c.router._loaded.length).toEqual(1);
 
                 c.router.unregister(5);
 
-                expect(c._.keys(c.router._registered).length).toEqual(4);
+                expect(_.keys(c.router._registered).length).toEqual(4);
                 expect(c.router._loaded.length).toEqual(0);
             });
 
@@ -100,7 +100,7 @@ define(['cilantro'], function(c) {
         describe('Routing', function() {
 
             it('should load views', function() {
-                expect(c.Backbone.history.navigate('foo/', {trigger: true})).toBe(true);
+                expect(Backbone.history.navigate('foo/', {trigger: true})).toBe(true);
 
                 // First two are loaded immediately since they are local views
                 expect(c.router._loaded.length).toEqual(2);
@@ -116,13 +116,13 @@ define(['cilantro'], function(c) {
             });
 
             it('should unload loaded modules', function() {
-                expect(c.Backbone.history.navigate('bar/', {trigger: true})).toBe(true);
+                expect(Backbone.history.navigate('bar/', {trigger: true})).toBe(true);
                 expect(c.router._loaded.length).toEqual(1);
 
                 children = $('#region3').children();
                 expect(children.length).toEqual(1);
 
-                expect(c.Backbone.history.navigate('foo/', {trigger: true})).toBe(true);
+                expect(Backbone.history.navigate('foo/', {trigger: true})).toBe(true);
 
                 // New element is added, but only the new one is visible
                 children = $('#region3').children();
@@ -152,13 +152,13 @@ define(['cilantro'], function(c) {
                 });
 
                 it('should trigger the load event', function() {
-                    c.Backbone.history.navigate('foo/', {trigger: true});
+                    Backbone.history.navigate('foo/', {trigger: true});
                     expect(loaded).toBe(true);
                 });
 
                 it('should trigger the unload event', function() {
-                    c.Backbone.history.navigate('foo/', {trigger: true});
-                    c.Backbone.history.navigate('bar/', {trigger: true});
+                    Backbone.history.navigate('foo/', {trigger: true});
+                    Backbone.history.navigate('bar/', {trigger: true});
                     expect(loaded).toBe(false);
                 });
             });

spec/route-spec-mod.js

@@ -1,3 +1,3 @@
-define(['cilantro'], function(c) {
-    return c.Backbone.View;
+define(['backbone'], function(Backbone) {
+    return Backbone.View;
 });

src/coffee/cilantro/core.coffee

@@ -1,7 +1,5 @@
 define [
-    'jquery'
     'underscore'
-    'backbone'
     'mediator'
     'promiser'
     'loglevel'
@@ -16,7 +14,7 @@ define [
     # Note, these are applied in place.
     'plugins/js'
     'plugins/jquery-ajax-queue'
-], ($, _, Backbone, mediator, promiser, loglevel, config, channels, utils, session, changelog) ->
+], (_, mediator, promiser, loglevel, config, channels, utils, session, changelog) ->
 
     c =
         # Version of cilantro
@@ -72,10 +70,5 @@ define [
     # Mediator channel topics for communication across the application
     channels = _.extend {}, channels, session.channels
 
-    # Additional properties to attach
-    # [DEPRECATED: 2.1.0] Require core libraries directly
-    props = { $, _, Backbone }
-
-    # Construct the base object which is composed core libraries, the
-    # mediator methods, session manager, and the config object
-    _.extend c, mediator, channels, props
+    # Mixin various components
+    _.extend c, mediator, channels

src/coffee/cilantro/models.coffee

@@ -1,5 +1,5 @@
 define [
-    './core'
+    'underscore'
     './models/field'
     './models/concept'
     './models/context'
@@ -9,6 +9,6 @@ define [
     './models/exporter'
     './models/query'
     './models/value'
-], (c, mods...) ->
+], (_, mods...) ->
 
-    c._.extend {}, mods...
+    _.extend {}, mods...

src/coffee/cilantro/models/base.coffee

@@ -1,8 +1,8 @@
 define [
-    '../core'
-], (c) ->
+    'backbone'
+], (Backbone) ->
 
-    class Model extends c.Backbone.Model
+    class Model extends Backbone.Model
         url: ->
             if @isNew() then super else @links.self
 
@@ -18,7 +18,7 @@ define [
             return attrs
 
 
-    class Collection extends c.Backbone.Collection
+    class Collection extends Backbone.Collection
         model: Model
 
         url: ->

src/coffee/cilantro/models/concept.coffee

@@ -1,8 +1,11 @@
 define [
-  '../core'
-  './base'
-  './field'
-], (c, base, field) ->
+    'jquery'
+    'underscore'
+    'backbone'
+    '../core'
+    './base'
+    './field'
+], ($, _, Backbone, c, base, field) ->
 
 
     class ConceptModel extends base.Model
@@ -37,8 +40,8 @@ define [
             c.session.url('concepts')
 
         search: (query, handler) ->
-            c.$.ajax
-                url: c._.result @, 'url'
+            $.ajax
+                url: _.result @, 'url'
                 data: query: query, brief: 1
                 dataType: 'json'
                 success: (resp) -> handler(resp)

src/coffee/cilantro/models/context.coffee

@@ -1,7 +1,7 @@
 define [
-    '../core'
+    'underscore'
     './context/nodes'
     './context/model'
-], (c, mods...) ->
+], (_, mods...) ->
 
-    c._.extend {}, mods...
+    _.extend {}, mods...

src/coffee/cilantro/models/context/manager.coffee

@@ -1,11 +1,12 @@
 define [
-    '../../core'
+    'underscore'
+    'backbone'
     './nodes'
-], (c, nodes) ->
+], (_, Backbone, nodes) ->
 
     class Events
 
-    c._.extend Events::, c.Backbone.Events
+    _.extend Events::, Backbone.Events
 
 
     # Light wrapper for fixing attrs for the top-level branch node. If `attrs`
@@ -30,7 +31,7 @@ define [
             'change:enabled': 'save'
 
         constructor: (@model, options) ->
-            @options = c._.extend({}, @options, options)
+            @options = _.extend({}, @options, options)
 
             # Define the working and upstream trees
             @working = new nodes.BranchNodeModel null,
@@ -76,7 +77,7 @@ define [
                 # later if more complex tree layouts are used.
                 return @_toJSON(node, options)
 
-            attrs = c._.clone(node.attributes)
+            attrs = _.clone(node.attributes)
 
             if node.type is 'branch'
                 children = []
@@ -104,7 +105,7 @@ define [
         update: (attrs) ->
             # Ensure the active and working trees are not empty, otherwise
             # change events do not fire.
-            attrs = c._.extend
+            attrs = _.extend
                 children: []
                 type: 'and'
             , attrs
@@ -135,11 +136,11 @@ define [
         # Define a node in the tree. Takes an option `type` which specifies
         # the node type to create.
         define: (attrs, path, options) ->
-            if not c._.isArray(path)
+            if not _.isArray(path)
                 options = path
                 path = []
 
-            options = c._.extend
+            options = _.extend
                 identKeys: @options.identKeys
             , options
 
@@ -157,15 +158,15 @@ define [
 
             # Get the identity of this node and add it to the parent
             parent.children.add(attrs, options)
-            return @find(c._.pick(attrs, options.identKeys))
+            return @find(_.pick(attrs, options.identKeys))
 
         # Save the model on behalf of a node.
         # TODO this assumes only a single node has been changed. If multiple
         # nodes are changed, only the node that triggers causes the save will
         # have it's events triggered.
         save: (node, options) ->
             # Trigger 'request' on node
-            options = c._.extend {}, options,
+            options = _.extend {}, options,
                 beforeSend: (xhr) =>
                     node.trigger('request', node, xhr, options)
 

src/coffee/cilantro/models/context/nodes.coffee

@@ -1,9 +1,9 @@
 define [
-    '../../core'
+    'underscore'
     './nodes/base'
     './nodes/condition'
     './nodes/branch'
     './nodes/composite'
-], (c, mods...) ->
+], (_, mods...) ->
 
-    c._.extend {}, mods...
+    _.extend {}, mods...