diff --git a/docs.json b/docs.json
index 36765298..eb68a22b 100644
--- a/docs.json
+++ b/docs.json
@@ -1,8 +1,9 @@
 {
   "title": "LoopBack Documentation",
   "content": [
-    "docs/api.md",    
-    "docs/api-app.md",
+    "lib/application.js",
+    {"title": "Middleware", "depth": 3},
+    "lib/middleware/token.js",
     "lib/models/access-token.js",
     "lib/models/access-context.js",
     "lib/models/acl.js",
diff --git a/docs/api-app.md b/docs/api-app.md
index 0b3c7bb8..28dbf87b 100644
--- a/docs/api-app.md
+++ b/docs/api-app.md
@@ -218,8 +218,6 @@ View generated REST documentation at [http://localhost:3000/_docs](http://localh
 
 LoopBack includes middleware similar to [Express / Connect middleware](http://expressjs.com/api.html#middleware).  
 
-
-
 #### loopback.token(options)
     
 **Options**
diff --git a/lib/application.js b/lib/application.js
index c7a19365..6497441f 100644
--- a/lib/application.js
+++ b/lib/application.js
@@ -1,4 +1,4 @@
-/**
+/*!
  * Module dependencies.
  */
 
@@ -12,13 +12,43 @@ var DataSource = require('loopback-datasource-juggler').DataSource
   , path = require('path');
 
 /**
+ * The `App` object represents a Loopback application.
+ * 
+ * The App object extends [Express](http://expressjs.com/api.html#express) and
+ * supports
+ * [Express / Connect middleware](http://expressjs.com/api.html#middleware). See
+ * [Express documentation](http://expressjs.com/api.html) for details.
+ * 
+ * ```js
+ * var loopback = require('loopback');
+ * var app = loopback();
+ * 
+ * app.get('/', function(req, res){
+ *   res.send('hello world');
+ * });
+ * 
+ * app.listen(3000);
+ * ```
+ * 
+ * @class LoopBackApplication
+ * @header app = loopback()
+ */
+function App() {
+  // no op
+}
+
+/*!
  * Export the app prototype.
  */
 
 var app = exports = module.exports = {};
 
 /**
- * Create a set of remote objects.
+ * Lazily load a set of [remote objects](http://apidocs.strongloop.com/strong-remoting/#remoteobjectsoptions).
+ *
+ * **NOTE:** Calling `app.remotes()` multiple times will only ever return a
+ * single set of remote objects.
+ * @returns {RemoteObjects}
  */
 
 app.remotes = function () {
@@ -29,7 +59,7 @@ app.remotes = function () {
   }
 }
 
-/**
+/*!
  * Remove a route by reference.
  */
 
@@ -44,9 +74,24 @@ app.disuse = function (route) {
 }
 
 /**
- * Expose a model.
+ * Define and attach a model to the app. The `Model` will be available on the
+ * `app.models` object.
  *
- * @param Model {Model}
+ * ```js
+ * var Widget = app.model('Widget', {dataSource: 'db'});
+ * Widget.create({name: 'pencil'});
+ * app.models.Widget.find(function(err, widgets) {
+ *   console.log(widgets[0]); // => {name: 'pencil'}
+ * });
+ * ```
+ * 
+ * @param {String} modelName The name of the model to define
+ * @options {Object} config The model's configuration
+ * @property {String} dataSource The `DataSource` to attach the model to
+ * @property {Object} [options] an object containing `Model` options
+ * @property {Object} [properties] object defining the `Model` properties in [LoopBack Definition Language](http://docs.strongloop.com/loopback-datasource-juggler/#loopback-definition-language)
+ * @end
+ * @returns {ModelConstructor} the model class
  */
 
 app.model = function (Model, config) {
@@ -78,6 +123,9 @@ app.model = function (Model, config) {
 
 /**
  * Get all exposed models.
+ *
+ * @header app.models() or app.models.ModelName
+ * @returns {Array} a list of model classes
  */
 
 app.models = function () {
@@ -86,6 +134,9 @@ app.models = function () {
 
 /**
  * Define a DataSource.
+ *
+ * @param {String} name The data source name
+ * @param {Object} config The data source config 
  */
 
 app.dataSource = function (name, config) {
@@ -121,7 +172,7 @@ app.remotes = function () {
   return this._remotes || (this._remotes = RemoteObjects.create());
 }
 
-/**
+/*!
  * Enable documentation
  */
  
@@ -189,8 +240,81 @@ app.enableAuth = function() {
 }
 
 /**
- * Initialize the app using JSON and JavaScript files.
- *
+ * Initialize an application from an options object or a set of JSON and JavaScript files.
+ * 
+ * **What happens during an app _boot_?**
+ * 
+ * 1. **DataSources** are created from an `options.dataSources` object or `datasources.json` in the current directory
+ * 2. **Models** are created from an `options.models` object or `models.json` in the current directory
+ * 3. Any JavaScript files in the `./models` directory are loaded with `require()`.
+ * 4. Any JavaScript files in the `./boot` directory are loaded with `require()`.
+ * 
+ * **Options**
+ * 
+ *  - `cwd` - _optional_ - the directory to use when loading JSON and JavaScript files
+ *  - `models` - _optional_ - an object containing `Model` definitions
+ *  - `dataSources` - _optional_ - an object containing `DataSource` definitions
+ * 
+ * <a name="model-definition"></a>
+ * **Model Definitions**
+ * 
+ * The following is an example of an object containing two `Model` definitions: "location" and "inventory".
+ * 
+ * ```js
+ * {
+ *   "dealership": {
+ *     // a reference, by name, to a dataSource definition
+ *     "dataSource": "my-db",
+ *     // the options passed to Model.extend(name, properties, options)
+ *     "options": {
+ *       "relations": {
+ *         "cars": {
+ *           "type": "hasMany",
+ *           "model": "Car",
+ *           "foreignKey": "dealerId"  
+ *         }
+ *       }
+ *     },
+ *     // the properties passed to Model.extend(name, properties, options)
+ *     "properties": {
+ *       "id": {"id": true},
+ *       "name": "String",
+ *       "zip": "Number",
+ *       "address": "String"
+ *     }
+ *   },
+ *   "car": {
+ *     "dataSource": "my-db"
+ *     "properties": {
+ *       "id": {
+ *         "type": "String",
+ *         "required": true,
+ *         "id": true
+ *       },
+ *       "make": {
+ *         "type": "String",
+ *         "required": true
+ *       },
+ *       "model": {
+ *         "type": "String",
+ *         "required": true
+ *       }
+ *     }
+ *   }
+ * }
+ * ```
+ * 
+ * **Model definition properties**
+ * 
+ *  - `dataSource` - **required** - a string containing the name of the data source definition to attach the `Model` to
+ *  - `options` - _optional_ - an object containing `Model` options
+ *  - `properties` _optional_ - an object defining the `Model` properties in [LoopBack Definition Language](http://docs.strongloop.com/loopback-datasource-juggler/#loopback-definition-language)
+ * 
+ * **DataSource definition properties**
+ *  
+ *  - `connector` - **required** - the name of the [connector](#working-with-data-sources-and-connectors)
+ * 
+ * 
  * @throws {Error} If config is not valid
  * @throws {Error} If boot fails
  */
diff --git a/lib/middleware/token.js b/lib/middleware/token.js
index 26088855..327989c1 100644
--- a/lib/middleware/token.js
+++ b/lib/middleware/token.js
@@ -1,4 +1,4 @@
-/**
+/*!
  * Module dependencies.
  */
 
@@ -6,12 +6,48 @@ var loopback = require('../loopback');
 var RemoteObjects = require('strong-remoting');
 var assert = require('assert');
 
-/**
+/*!
  * Export the middleware.
  */
 
 module.exports = token;
 
+/**    
+ * **Options**
+ * 
+ *  - `cookies` - An `Array` of cookie names
+ *  - `headers` - An `Array` of header names
+ *  - `params` - An `Array` of param names
+ *  - `model` - Specify an AccessToken class to use
+ * 
+ * Each array is used to add additional keys to find an `accessToken` for a `request`.
+ * 
+ * The following example illustrates how to check for an `accessToken` in a custom cookie, query string parameter
+ * and header called `foo-auth`.
+ * 
+ * ```js
+ * app.use(loopback.token({
+ *   cookies: ['foo-auth'],
+ *   headers: ['foo-auth', 'X-Foo-Auth'],
+ *   cookies: ['foo-auth', 'foo_auth']
+ * }));
+ * ```
+ * 
+ * **Defaults**
+ * 
+ * By default the following names will be checked. These names are appended to any optional names. They will always
+ * be checked, but any names specified will be checked first.
+ * 
+ * - **access_token**
+ * - **X-Access-Token**
+ * - **authorization**
+ * - **access_token**
+ * 
+ * **NOTE:** The `loopback.token()` middleware will only check for [signed cookies](http://expressjs.com/api.html#req.signedCookies).
+ *
+ * @header loopback.token(options)
+ */
+
 function token(options) {
   options = options || {};
   var TokenModel = options.model || loopback.AccessToken;
diff --git a/lib/models/access-token.js b/lib/models/access-token.js
index fba53357..acf8484e 100644
--- a/lib/models/access-token.js
+++ b/lib/models/access-token.js
@@ -12,12 +12,8 @@ var Model = require('../loopback').Model
   , Role = require('./role').Role
   , ACL = require('./acl').ACL;
 
-/**
+/*!
  * Default AccessToken properties.
- * 
- * @property id {String} - Generated token ID
- * @property ttl {Number} - Time to live
- * @property created {Date} - When the token was created
  */
 
 var properties = {
@@ -30,6 +26,10 @@ var properties = {
 
 /**
  * Token based authentication and access control.
+ *
+ * @property id {String} Generated token ID
+ * @property ttl {Number} Time to live
+ * @property created {Date} When the token was created
  * 
  * **Default ACLs**
  *