diff --git a/Gruntfile.js b/Gruntfile.js
index 317cb7eba..ee49ae9eb 100644
--- a/Gruntfile.js
+++ b/Gruntfile.js
@@ -430,7 +430,11 @@ module.exports = function(grunt) {
         },
         jsdoc : {
             runtimeAPI: {
-                src: 'packages/node_modules/@node-red/runtime/lib/api/*.js',
+                src: [
+                    'packages/node_modules/node-red/lib/red.js',
+                    'packages/node_modules/@node-red/runtime/lib/index.js',
+                    'packages/node_modules/@node-red/runtime/lib/api/*.js',
+                    ],
                 options: {
                     destination: 'docs',
                     configure: './jsdoc.json'
@@ -449,7 +453,8 @@ module.exports = function(grunt) {
                 options: {
                     separators: true
                 },
-                src: 'packages/node_modules/@node-red/runtime/lib/api/*.js',
+                src: ['packages/node_modules/@node-red/runtime/lib/index.js',
+                      'packages/node_modules/@node-red/runtime/lib/api/*.js'],
                 dest: 'packages/node_modules/@node-red/runtime/docs/api.md'
             },
             nodeREDUtil: {
diff --git a/packages/node_modules/@node-red/editor-api/lib/index.js b/packages/node_modules/@node-red/editor-api/lib/index.js
index 51fd1079c..3450eaafb 100644
--- a/packages/node_modules/@node-red/editor-api/lib/index.js
+++ b/packages/node_modules/@node-red/editor-api/lib/index.js
@@ -28,7 +28,7 @@ var adminApp;
 var server;
 var editor;
 
-function init(_server,settings,storage,runtimeAPI) {
+function init(settings,_server,storage,runtimeAPI) {
     server = _server;
     if (settings.httpAdminRoot !== false) {
         adminApp = express();
@@ -100,6 +100,5 @@ module.exports = {
     auth: {
         needsPermission: auth.needsPermission
     },
-    get adminApp() { return adminApp; },
-    get server() { return server; }
+    get adminApp() { return adminApp; }
 };
diff --git a/packages/node_modules/@node-red/registry/lib/loader.js b/packages/node_modules/@node-red/registry/lib/loader.js
index 7f737e3d5..901a7fba5 100644
--- a/packages/node_modules/@node-red/registry/lib/loader.js
+++ b/packages/node_modules/@node-red/registry/lib/loader.js
@@ -98,7 +98,9 @@ function createNodeApi(node) {
             register: function(type) {
                 return runtime.library.register(node.id,type);
             }
-        }
+        },
+        httpNode: runtime.nodeApp,
+        server: runtime.server
     }
     copyObjectProperties(runtime.nodes,red.nodes,["createNode","getNode","eachNode","addCredentials","getCredentials","deleteCredentials" ]);
     red.nodes.registerType = function(type,constructor,opts) {
@@ -109,8 +111,6 @@ function createNodeApi(node) {
     if (runtime.adminApi) {
         red.auth = runtime.adminApi.auth;
         red.httpAdmin = runtime.adminApi.adminApp;
-        red.httpNode = runtime.nodeApp;
-        red.server = runtime.server;
     } else {
         //TODO: runtime.adminApi is always stubbed if not enabled, so this block
         // is unused - but may be needed for the unit tests
diff --git a/packages/node_modules/@node-red/runtime/lib/api/comms.js b/packages/node_modules/@node-red/runtime/lib/api/comms.js
index 7713fd3dc..079f75c14 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/comms.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/comms.js
@@ -15,7 +15,8 @@
  **/
 
 /**
- * @namespace RED.comms
+ * This is the comms subsystem of the runtime.
+ * @mixin @node-red/runtime_comms
  */
 
 /**
@@ -89,7 +90,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {CommsConnection} opts.client - the client connection
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.comms
+    * @memberof @node-red/runtime_comms
     */
     addConnection: function(opts) {
         connections.push(opts.client);
@@ -102,7 +103,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {CommsConnection} opts.client - the client connection
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.comms
+    * @memberof @node-red/runtime_comms
     */
     removeConnection: function(opts) {
         for (var i=0;i<connections.length;i++) {
@@ -123,7 +124,7 @@ var api = module.exports = {
     * @param {CommsConnection} opts.client - the client connection
     * @param {String} opts.topic - the topic to subscribe to
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.comms
+    * @memberof @node-red/runtime_comms
     */
     subscribe: function(opts) {
         var re = new RegExp("^"+opts.topic.replace(/([\[\]\?\(\)\\\\$\^\*\.|])/g,"\\$1").replace(/\+/g,"[^/]+").replace(/\/#$/,"(\/.*)?")+"$");
@@ -142,7 +143,7 @@ var api = module.exports = {
     * @param {CommsConnection} opts.client - the client connection
     * @param {String} opts.topic - the topic to unsubscribe from
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.comms
+    * @memberof @node-red/runtime_comms
     */
     unsubscribe: function(opts) {}
 };
diff --git a/packages/node_modules/@node-red/runtime/lib/api/context.js b/packages/node_modules/@node-red/runtime/lib/api/context.js
index cbe665e53..0b2fefcc9 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/context.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/context.js
@@ -15,7 +15,7 @@
  **/
 
 /**
- * @namespace RED.context
+ * @mixin @node-red/runtime_context
  */
 
 var runtime;
@@ -69,7 +69,7 @@ var api = module.exports = {
     * @param {String} opts.key - the context key
 
     * @return {Promise} - the node information
-    * @memberof RED.context
+    * @memberof @node-red/runtime_context
     */
     getValue: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -163,7 +163,7 @@ var api = module.exports = {
     * @param {String} opts.key - the context key
 
     * @return {Promise} - the node information
-    * @memberof RED.context
+    * @memberof @node-red/runtime_context
     */
     delete: function(opts) {
         return new Promise(function(resolve,reject) {
diff --git a/packages/node_modules/@node-red/runtime/lib/api/flows.js b/packages/node_modules/@node-red/runtime/lib/api/flows.js
index a96fdd9a3..735e295fc 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/flows.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/flows.js
@@ -15,7 +15,7 @@
  **/
 
  /**
-  * @namespace RED.flows
+  * @mixin @node-red/runtime_flows
   */
 
 /**
@@ -44,7 +44,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Flows>} - the active flow configuration
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     getFlows: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -57,7 +57,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Flows>} - the active flow configuration
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     setFlows: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -99,7 +99,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {Object} opts.flow - the flow to add
     * @return {Promise<String>} - the id of the added flow
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     addFlow: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -123,7 +123,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {Object} opts.id - the id of the flow to retrieve
     * @return {Promise<Flow>} - the active flow configuration
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     getFlow: function(opts) {
         return new Promise(function (resolve,reject) {
@@ -148,7 +148,7 @@ var api = module.exports = {
     * @param {Object} opts.id - the id of the flow to update
     * @param {Object} opts.flow - the flow configuration
     * @return {Promise<String>} - the id of the updated flow
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     updateFlow: function(opts) {
         return new Promise(function (resolve,reject) {
@@ -185,7 +185,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {Object} opts.id - the id of the flow to delete
     * @return {Promise} - resolves if successful
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     deleteFlow: function(opts) {
         return new Promise(function (resolve,reject) {
@@ -222,7 +222,7 @@ var api = module.exports = {
     * @param {String} opts.type - the node type to return the credential information for
     * @param {String} opts.id - the node id
     * @return {Promise<Object>} - the safe credentials
-    * @memberof RED.flows
+    * @memberof @node-red/runtime_flows
     */
     getNodeCredentials: function(opts) {
         return new Promise(function(resolve,reject) {
diff --git a/packages/node_modules/@node-red/runtime/lib/api/index.js b/packages/node_modules/@node-red/runtime/lib/api/index.js
index 2b315c0dc..8856ac3c2 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/index.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/index.js
@@ -17,13 +17,7 @@
 
 
 var runtime;
-/**
- * This module provides the core runtime component of Node-RED.
- * It does *not* include the Node-RED editor. All interaction with
- * this module is done using the api provided.
- *
- * @namespace RED
- */
+
 var api = module.exports = {
     init: function(_runtime) {
         runtime = _runtime;
@@ -44,31 +38,10 @@ var api = module.exports = {
     projects: require("./projects"),
     context: require("./context"),
 
-    /**
-    * Returns whether the runtime is started
-    * @param {Object} opts
-    * @param {User} opts.user - the user calling the api
-    * @return {Promise<Boolean>} - whether the runtime is started
-    * @memberof RED
-    */
     isStarted: function(opts) {
         return Promise.resolve(runtime.isStarted());
     },
-
-    /**
-    * Returns version number of the runtime
-    * @param {Object} opts
-    * @param {User} opts.user - the user calling the api
-    * @return {Promise<String>} - the runtime version number
-    * @memberof RED
-    */
     version: function(opts) {
         return Promise.resolve(runtime.version());
     }
 }
-
-/**
- * A user accessing the API
- * @typedef User
- * @type {object}
- */
diff --git a/packages/node_modules/@node-red/runtime/lib/api/library.js b/packages/node_modules/@node-red/runtime/lib/api/library.js
index f6d521b10..6f6571463 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/library.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/library.js
@@ -15,7 +15,7 @@
  **/
 
 /**
- * @namespace RED.library
+ * @mixin @node-red/runtime_library
  */
 
 var runtime;
@@ -32,7 +32,7 @@ var api = module.exports = {
     * @param {String} opts.type - the type of entry
     * @param {String} opts.path - the path of the entry
     * @return {Promise<String|Object>} - resolves when complete
-    * @memberof RED.library
+    * @memberof @node-red/runtime_library
     */
     getEntry: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -71,7 +71,7 @@ var api = module.exports = {
     * @param {Object} opts.meta - any meta data associated with the entry
     * @param {String} opts.body - the body of the entry
     * @return {Promise} - resolves when complete
-    * @memberof RED.library
+    * @memberof @node-red/runtime_library
     */
     saveEntry: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -98,7 +98,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.type - the type of entry
     * @return {Promise<Object>} - the entry listing
-    * @memberof RED.library
+    * @memberof @node-red/runtime_library
     */
     getEntries: function(opts) {
         return new Promise(function(resolve,reject) {
diff --git a/packages/node_modules/@node-red/runtime/lib/api/nodes.js b/packages/node_modules/@node-red/runtime/lib/api/nodes.js
index bc7b2c36b..ca67acc17 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/nodes.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/nodes.js
@@ -15,7 +15,7 @@
  **/
 
 /**
- * @namespace RED.nodes
+ * @mixin @node-red/runtime_nodes
  */
 
 var fs = require("fs");
@@ -49,7 +49,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the node set to return
     * @return {Promise<NodeInfo>} - the node information
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getNodeInfo: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -74,7 +74,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<NodeList>} - the list of node modules
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getNodeList: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -90,7 +90,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the node set to return
     * @param {String} opts.lang - the locale language to return
     * @return {Promise<String>} - the node html content
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getNodeConfig: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -115,7 +115,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.lang - the locale language to return
     * @return {Promise<String>} - the node html content
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getNodeConfigs: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -130,7 +130,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.module - the id of the module to return
     * @return {Promise<ModuleInfo>} - the node module info
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getModuleInfo: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -155,7 +155,7 @@ var api = module.exports = {
     * @param {String} opts.module - the id of the module to install
     * @param {String} opts.version - (optional) the version of the module to install
     * @return {Promise<ModuleInfo>} - the node module info
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     addModule: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -210,7 +210,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.module - the id of the module to remove
     * @return {Promise} - resolves when complete
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     removeModule: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -253,7 +253,7 @@ var api = module.exports = {
     * @param {String} opts.module - the id of the module to enable or disable
     * @param {String} opts.enabled - whether the module should be enabled or disabled
     * @return {Promise<ModuleInfo>} - the module info object
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     setModuleState: function(opts) {
         var mod = opts.module;
@@ -301,7 +301,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the node-set to enable or disable
     * @param {String} opts.enabled - whether the module should be enabled or disabled
     * @return {Promise<ModuleInfo>} - the module info object
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     setNodeSetState: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -348,7 +348,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {User} opts.lang - the i18n language to return. If not set, uses runtime default (en-US)
     * @return {Promise<Object>} - the message catalogs
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getModuleCatalogs: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -377,7 +377,7 @@ var api = module.exports = {
     * @param {User} opts.module - the module
     * @param {User} opts.lang - the i18n language to return. If not set, uses runtime default (en-US)
     * @return {Promise<Object>} - the message catalog
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getModuleCatalog: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -398,7 +398,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<IconList>} - the list of all icons
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getIconList: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -414,7 +414,7 @@ var api = module.exports = {
     * @param {String} opts.module - the id of the module requesting the icon
     * @param {String} opts.icon - the name of the icon
     * @return {Promise<Buffer>} - the icon file as a Buffer or null if no icon available
-    * @memberof RED.nodes
+    * @memberof @node-red/runtime_nodes
     */
     getIcon: function(opts) {
         return new Promise(function(resolve,reject) {
diff --git a/packages/node_modules/@node-red/runtime/lib/api/projects.js b/packages/node_modules/@node-red/runtime/lib/api/projects.js
index 79b447d52..27aef8c7b 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/projects.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/projects.js
@@ -15,7 +15,7 @@
  **/
 
 /**
- * @namespace RED.projects
+ * @mixin @node-red/runtime_projects
  */
 
 var runtime;
@@ -33,7 +33,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     listProjects: function(opts) {
         return runtime.storage.projects.listProjects(opts.user).then(function(list) {
@@ -57,7 +57,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {Object} opts.project - the project information
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     createProject: function(opts) {
         return runtime.storage.projects.createProject(opts.user, opts.project)
@@ -70,7 +70,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project to initialise
     * @param {Object} opts.project - the project information
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     initialiseProject: function(opts) {
         // Initialised set when creating default files for an empty repo
@@ -82,7 +82,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Object>} - the active project
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getActiveProject: function(opts) {
         return Promise.resolve(runtime.storage.projects.getActiveProject(opts.user));
@@ -94,7 +94,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the project to activate
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     setActiveProject: function(opts) {
         var currentProject = runtime.storage.projects.getActiveProject(opts.user);
@@ -111,7 +111,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the project to get
     * @return {Promise<Object>} - the project metadata
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getProject: function(opts) {
         return runtime.storage.projects.getProject(opts.user, opts.id)
@@ -124,7 +124,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project to update
     * @param {Object} opts.project - the project information
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     updateProject: function(opts) {
         return runtime.storage.projects.updateProject(opts.user, opts.id, opts.project);
@@ -136,7 +136,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the project to update
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     deleteProject: function(opts) {
         return runtime.storage.projects.deleteProject(opts.user, opts.id);
@@ -149,7 +149,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {Boolean} opts.remote - whether to include status of remote repos
     * @return {Promise<Object>} - the project status
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getStatus: function(opts) {
         return runtime.storage.projects.getStatus(opts.user, opts.id, opts.remote)
@@ -162,7 +162,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {Boolean} opts.remote - whether to return remote branches (true) or local (false)
     * @return {Promise<Object>} - a list of the local branches
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getBranches: function(opts) {
         return runtime.storage.projects.getBranches(opts.user, opts.id, opts.remote);
@@ -175,7 +175,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String} opts.branch - the name of the branch
     * @return {Promise<Object>} - the status of the branch
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getBranchStatus: function(opts) {
         return runtime.storage.projects.getBranchStatus(opts.user, opts.id, opts.branch);
@@ -189,7 +189,7 @@ var api = module.exports = {
     * @param {String} opts.branch - the name of the branch
     * @param {Boolean} opts.create - whether to create the branch if it doesn't exist
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     setBranch: function(opts) {
         return runtime.storage.projects.setBranch(opts.user, opts.id, opts.branch, opts.create)
@@ -203,7 +203,7 @@ var api = module.exports = {
     * @param {String} opts.branch - the name of the branch
     * @param {Boolean} opts.force - whether to force delete
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     deleteBranch: function(opts) {
         return runtime.storage.projects.deleteBranch(opts.user, opts.id, opts.branch, false, opts.force);
@@ -216,7 +216,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String} opts.message - the message to associate with the commit
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     commit: function(opts) {
         return runtime.storage.projects.commit(opts.user, opts.id,{message: opts.message});
@@ -229,7 +229,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String} opts.sha - the sha of the commit to return
     * @return {Promise<Object>} - the commit details
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getCommit: function(opts) {
         return runtime.storage.projects.getCommit(opts.user, opts.id, opts.sha);
@@ -243,7 +243,7 @@ var api = module.exports = {
     * @param {String} opts.limit - limit how many to return
     * @param {String} opts.before - id of the commit to work back from
     * @return {Promise<Array>} - an array of commits
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getCommits: function(opts) {
         return runtime.storage.projects.getCommits(opts.user, opts.id, {
@@ -258,7 +258,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the project
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     abortMerge: function(opts) {
         return runtime.storage.projects.abortMerge(opts.user, opts.id);
@@ -272,7 +272,7 @@ var api = module.exports = {
     * @param {String} opts.path - the path of the file being merged
     * @param {String} opts.resolutions - how to resolve the merge conflict
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     resolveMerge: function(opts) {
         return runtime.storage.projects.resolveMerge(opts.user, opts.id, opts.path, opts.resolution);
@@ -284,7 +284,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the project
     * @return {Promise<Object>} - the file listing
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getFiles: function(opts) {
         return runtime.storage.projects.getFiles(opts.user, opts.id);
@@ -298,7 +298,7 @@ var api = module.exports = {
     * @param {String} opts.path - the path of the file
     * @param {String} opts.tree - the version control tree to use
     * @return {Promise<String>} - the content of the file
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getFile: function(opts) {
         return runtime.storage.projects.getFile(opts.user, opts.id,opts.path,opts.tree);
@@ -311,7 +311,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String|Array} opts.path - the path of the file, or an array of paths
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     stageFile: function(opts) {
         return runtime.storage.projects.stageFile(opts.user, opts.id, opts.path);
@@ -324,7 +324,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String} opts.path - the path of the file. If not set, all staged files are unstaged
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     unstageFile: function(opts) {
         return runtime.storage.projects.unstageFile(opts.user, opts.id, opts.path);
@@ -337,7 +337,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String} opts.path - the path of the file
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     revertFile: function(opts) {
         return runtime.storage.projects.revertFile(opts.user, opts.id,opts.path)
@@ -351,7 +351,7 @@ var api = module.exports = {
     * @param {String} opts.path - the path of the file
     * @param {String} opts.type - the type of diff
     * @return {Promise<Object>} - the requested diff
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getFileDiff: function(opts) {
         return runtime.storage.projects.getFileDiff(opts.user, opts.id, opts.path, opts.type);
@@ -363,7 +363,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {String} opts.id - the id of the project
     * @return {Promise<Object>} - a list of project remotes
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     getRemotes: function(opts) {
         return runtime.storage.projects.getRemotes(opts.user, opts.id);
@@ -379,7 +379,7 @@ var api = module.exports = {
     * @param {String} opts.remote.name - the name of the remote
     * @param {String} opts.remote.url - the url of the remote
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     addRemote: function(opts) {
         return runtime.storage.projects.addRemote(opts.user, opts.id, opts.remote)
@@ -392,7 +392,7 @@ var api = module.exports = {
     * @param {String} opts.id - the id of the project
     * @param {String} opts.remote - the name of the remote
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     removeRemote: function(opts) {
         return runtime.storage.projects.removeRemote(opts.user, opts.id, opts.remote);
@@ -406,7 +406,7 @@ var api = module.exports = {
     * @param {Object} opts.remote - the remote metadata
     * @param {String} opts.remote.name - the name of the remote
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     updateRemote: function(opts) {
         return runtime.storage.projects.updateRemote(opts.user, opts.id, opts.remote.name, opts.remote)
@@ -417,7 +417,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     pull: function(opts) {
         return runtime.storage.projects.pull(opts.user, opts.id, opts.remote, opts.track, opts.allowUnrelatedHistories);
@@ -431,7 +431,7 @@ var api = module.exports = {
     * @param {String} opts.remote - the name of the remote
     * @param {String} opts.track - whether to set the remote as the upstream
     * @return {Promise<Object>} - resolves when complete
-    * @memberof RED.projects
+    * @memberof @node-red/runtime_projects
     */
     push: function(opts) {
         return runtime.storage.projects.push(opts.user, opts.id, opts.remote, opts.track);
diff --git a/packages/node_modules/@node-red/runtime/lib/api/settings.js b/packages/node_modules/@node-red/runtime/lib/api/settings.js
index 9afbff827..3ae83d0cf 100644
--- a/packages/node_modules/@node-red/runtime/lib/api/settings.js
+++ b/packages/node_modules/@node-red/runtime/lib/api/settings.js
@@ -15,7 +15,7 @@
  **/
 
 /**
- * @namespace RED.settings
+ * @mixin @node-red/runtime_settings
  */
 
 var util = require("util");
@@ -61,7 +61,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Object>} - the runtime settings
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     getRuntimeSettings: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -126,7 +126,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Object>} - the user settings
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     getUserSettings: function(opts) {
         var username;
@@ -144,7 +144,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {Object} opts.settings - the updates to the user settings
     * @return {Promise<Object>} - the user settings
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     updateUserSettings: function(opts) {
         var username;
@@ -179,7 +179,7 @@ var api = module.exports = {
     * @param {Object} opts
     * @param {User} opts.user - the user calling the api
     * @return {Promise<Object>} - the user's ssh keys
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     getUserKeys: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -199,7 +199,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {User} opts.id - the id of the key to return
     * @return {Promise<String>} - the user's ssh public key
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     getUserKey: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -230,7 +230,7 @@ var api = module.exports = {
     * @param {User} opts.comment - (option) a comment to associate with the key pair
     * @param {User} opts.size - (optional) the size of the key. Default: 2048
     * @return {Promise<String>} - the id of the generated key
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     generateUserKey: function(opts) {
         return new Promise(function(resolve,reject) {
@@ -250,7 +250,7 @@ var api = module.exports = {
     * @param {User} opts.user - the user calling the api
     * @param {User} opts.id - the id of the key to delete
     * @return {Promise} - resolves when deleted
-    * @memberof RED.settings
+    * @memberof @node-red/runtime_settings
     */
     removeUserKey: function(opts) {
         return new Promise(function(resolve,reject) {
diff --git a/packages/node_modules/@node-red/runtime/lib/index.js b/packages/node_modules/@node-red/runtime/lib/index.js
index 2ca92a4f0..4cd257f0f 100644
--- a/packages/node_modules/@node-red/runtime/lib/index.js
+++ b/packages/node_modules/@node-red/runtime/lib/index.js
@@ -1,4 +1,4 @@
-/**
+/*!
  * Copyright JS Foundation and other contributors, http://js.foundation
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -31,8 +31,8 @@ var fs = require("fs");
 var os = require("os");
 
 var redUtil = require("@node-red/util");
-var log;
-var i18n;
+var log = redUtil.log;
+var i18n = redUtil.i18n;
 
 var runtimeMetricInterval = null;
 
@@ -48,18 +48,24 @@ var adminApi = {
     auth: {
         needsPermission: function() {}
     },
-    comms: {
-        publish: function() {}
-    },
     adminApp: stubbedExpressApp,
     server: {}
 }
 
 var nodeApp;
+var server;
 
-function init(userSettings,_adminApi) {
-    log = redUtil.log;
-    i18n = redUtil.i18n;
+
+/**
+ * Initialise the runtime module.
+ * @param {Object} settings - the runtime settings object
+ * @param {HTTPServer} server - the http server instance for the server to use
+ * @param {AdminAPI} adminApi - an instance of @node-red/editor-api. <B>TODO</B>: This needs to be
+ *                              better abstracted.
+ * @memberof @node-red/runtime
+ */
+function init(userSettings,httpServer,_adminApi) {
+    server = httpServer;
     userSettings.version = getVersion();
     settings.init(userSettings);
 
@@ -90,6 +96,12 @@ function getVersion() {
     return version;
 }
 
+/**
+ * Start the runtime.
+ * @return {Promise} - resolves when the runtime is started. This does not mean the
+ *   flows will be running as they are started asynchronously.
+ * @memberof @node-red/runtime
+ */
 function start() {
 
     return i18n.registerMessageCatalog("runtime",path.resolve(path.join(__dirname,"..","locales")),"runtime.json")
@@ -225,6 +237,11 @@ function reportMetrics() {
     });
 }
 
+/**
+ * Stops the runtime.
+ * @return {Promise} - resolves when the runtime is stopped.
+ * @memberof @node-red/runtime
+ */
 function stop() {
     if (runtimeMetricInterval) {
         clearInterval(runtimeMetricInterval);
@@ -253,27 +270,89 @@ var runtime = {
     util: require("@node-red/util").util,
     get adminApi() { return adminApi },
     get nodeApp() { return nodeApp },
+    get server() { return server },
     isStarted: function() {
         return started;
     }
 };
 
-
+/**
+ * This module provides the core runtime component of Node-RED.
+ * It does *not* include the Node-RED editor. All interaction with
+ * this module is done using the api provided.
+ *
+ * @namespace @node-red/runtime
+ */
 module.exports = {
     init: init,
     start: start,
     stop: stop,
 
-    "_": runtime,
-
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_comms
+    */
     comms: externalAPI.comms,
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_flows
+    */
     flows: externalAPI.flows,
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_library
+    */
     library: externalAPI.library,
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_nodes
+    */
     nodes: externalAPI.nodes,
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_settings
+    */
     settings: externalAPI.settings,
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_projects
+    */
     projects: externalAPI.projects,
+    /**
+    * @memberof @node-red/runtime
+    * @mixes @node-red/runtime_context
+    */
     context: externalAPI.context,
 
+    /**
+    * Returns whether the runtime is started
+    * @param {Object} opts
+    * @param {User} opts.user - the user calling the api
+    * @return {Promise<Boolean>} - whether the runtime is started
+    * @function
+    * @memberof @node-red/runtime
+    */
     isStarted: externalAPI.isStarted,
-    version: externalAPI.version
+
+    /**
+    * Returns version number of the runtime
+    * @param {Object} opts
+    * @param {User} opts.user - the user calling the api
+    * @return {Promise<String>} - the runtime version number
+    * @function
+    * @memberof @node-red/runtime
+    */
+    version: externalAPI.version,
+
+    storage: storage,
+    events: events,
+    get httpNode() { return nodeApp },
+    get server() { return server }
 }
+
+
+/**
+ * A user accessing the API
+ * @typedef User
+ * @type {object}
+ */
diff --git a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/Project.js b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/Project.js
index f580c178e..d07a544c8 100644
--- a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/Project.js
+++ b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/Project.js
@@ -26,7 +26,7 @@ var defaultFileSet = require("./defaultFileSet");
 var sshKeys = require("./ssh");
 var settings;
 var runtime;
-var log;
+var log = require("@node-red/util").log;
 
 var projectsDir;
 
@@ -162,7 +162,7 @@ Project.prototype.initialise = function(user,data) {
         if (defaultFileSet.hasOwnProperty(file)) {
             var path = fspath.join(project.path,file);
             if (!fs.existsSync(path)) {
-                promises.push(util.writeFile(path,defaultFileSet[file](project, runtime)));
+                promises.push(util.writeFile(path,defaultFileSet[file](project)));
             }
 
         }
@@ -858,7 +858,7 @@ function createDefaultProject(user, project) {
         }
         for (var file in defaultFileSet) {
             if (defaultFileSet.hasOwnProperty(file)) {
-                promises.push(util.writeFile(fspath.join(projectPath,file),defaultFileSet[file](project, runtime)));
+                promises.push(util.writeFile(fspath.join(projectPath,file),defaultFileSet[file](project)));
             }
         }
 
@@ -992,7 +992,6 @@ function loadProject(projectPath) {
 function init(_settings, _runtime) {
     settings = _settings;
     runtime = _runtime;
-    log = runtime.log;
     projectsDir = fspath.join(settings.userDir,"projects");
     authCache.init();
 }
diff --git a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/defaultFileSet.js b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/defaultFileSet.js
index a7e825207..04b95e3e0 100644
--- a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/defaultFileSet.js
+++ b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/defaultFileSet.js
@@ -14,9 +14,10 @@
  * limitations under the License.
  **/
 
+var i18n = require("@node-red/util").i18n;
+
 module.exports = {
-    "package.json": function(project, runtime) {
-        var i18n = runtime.i18n;
+    "package.json": function(project) {
         var package = {
             "name": project.name,
             "description": project.summary||i18n._("storage.localfilesystem.projects.summary"),
@@ -35,8 +36,7 @@ module.exports = {
         }
         return JSON.stringify(package,"",4);
     },
-    "README.md": function(project, runtime) {
-        var i18n = runtime.i18n;
+    "README.md": function(project) {
         var content = project.name+"\n"+("=".repeat(project.name.length))+"\n\n";
         if (project.summary) {
             content += project.summary+"\n\n";
diff --git a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/git/index.js b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/git/index.js
index d5c23ccb6..214a9e615 100644
--- a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/git/index.js
+++ b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/git/index.js
@@ -25,7 +25,7 @@ var path = require("path");
 
 var gitCommand = "git";
 var gitVersion;
-var log;
+var log = require("@node-red/util").log;
 
 function runGitCommand(args,cwd,env,emit) {
     log.trace(gitCommand + JSON.stringify(args));
@@ -382,8 +382,7 @@ function removeRemote(cwd,name) {
 }
 
 module.exports = {
-    init: function(_settings,_runtime) {
-        log = _runtime.log
+    init: function(_settings) {
         return new Promise(function(resolve,reject) {
             Promise.all([
                 runGitCommand(["--version"]),
diff --git a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/index.js b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/index.js
index d11c2b06d..4fee06a45 100644
--- a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/index.js
+++ b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/index.js
@@ -29,7 +29,7 @@ var Projects = require("./Project");
 
 var settings;
 var runtime;
-var log;
+var log = require("@node-red/util").log;
 
 var projectsEnabled = false;
 var projectLogMessages = [];
@@ -42,7 +42,6 @@ var globalGitUser = false;
 function init(_settings, _runtime) {
     settings = _settings;
     runtime = _runtime;
-    log = runtime.log;
 
     try {
         if (settings.editorTheme.projects.enabled === true) {
@@ -90,7 +89,7 @@ function init(_settings, _runtime) {
 
     if (projectsEnabled) {
         return sshTools.init(settings,runtime).then(function() {
-            gitTools.init(_settings, _runtime).then(function(gitConfig) {
+            gitTools.init(_settings).then(function(gitConfig) {
                 if (!gitConfig || /^1\./.test(gitConfig.version)) {
                     if (!gitConfig) {
                         projectLogMessages.push(log._("storage.localfilesystem.projects.git-not-found"))
@@ -109,7 +108,7 @@ function init(_settings, _runtime) {
                 } else {
                     globalGitUser = gitConfig.user;
                     Projects.init(settings,runtime);
-                    sshTools.init(settings,runtime);
+                    sshTools.init(settings);
                     projectsDir = fspath.join(settings.userDir,"projects");
                     if (!settings.readOnly) {
                         return fs.ensureDir(projectsDir)
diff --git a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/index.js b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/index.js
index cc9bd8754..25dacd3b1 100644
--- a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/index.js
+++ b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/index.js
@@ -20,15 +20,12 @@ var fspath = require("path");
 var keygen = require("./keygen");
 
 var settings;
-var runtime;
-var log;
+var log = require("@node-red/util").log;
 var sshkeyDir;
 var userSSHKeyDir;
 
-function init(_settings, _runtime) {
+function init(_settings) {
     settings = _settings;
-    runtime = _runtime;
-    log = runtime.log;
     sshkeyDir = fspath.resolve(fspath.join(settings.userDir, "projects", ".sshkeys"));
     userSSHKeyDir = fspath.join(process.env.HOME || process.env.USERPROFILE || process.env.HOMEPATH, ".ssh");
     // console.log('sshkeys.init()');
diff --git a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/keygen.js b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/keygen.js
index d7081c154..218144c12 100644
--- a/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/keygen.js
+++ b/packages/node_modules/@node-red/runtime/lib/storage/localfilesystem/projects/ssh/keygen.js
@@ -18,7 +18,7 @@ var child_process = require('child_process');
 
 var sshkeygenCommand = "ssh-keygen";
 
-var log;
+var log = require("@node-red/util").log;
 
 function runSshKeygenCommand(args,cwd,env) {
     return new Promise(function(resolve, reject) {
@@ -54,10 +54,6 @@ function runSshKeygenCommand(args,cwd,env) {
     });
 }
 
-function init(_settings, _runtime) {
-    log = _runtime.log;
-}
-
 function generateKey(options) {
     var args = ['-q', '-t', 'rsa'];
     var err;
@@ -90,6 +86,5 @@ function generateKey(options) {
 }
 
 module.exports = {
-    init: init,
-    generateKey: generateKey,
+    generateKey: generateKey
 };
diff --git a/packages/node_modules/node-red/lib/red.js b/packages/node_modules/node-red/lib/red.js
index 128869c43..2dcc1ae53 100644
--- a/packages/node_modules/node-red/lib/red.js
+++ b/packages/node_modules/node-red/lib/red.js
@@ -1,4 +1,4 @@
-/**
+/*!
  * Copyright JS Foundation and other contributors, http://js.foundation
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -22,8 +22,6 @@ var redUtil = require("@node-red/util");
 
 var api = require("@node-red/editor-api");
 
-var nodeApp = null;
-var adminApp = null;
 var server = null;
 var apiEnabled = false;
 
@@ -37,9 +35,20 @@ function checkVersion(userSettings) {
         userSettings.UNSUPPORTED_VERSION = process.version;
     }
 }
-
+/**
+ * This module provides the full Node-RED application, with both the runtime
+ * and editor components built in.
+ *
+ * @namespace node-red
+ */
 module.exports = {
-    init: function(httpServer,userSettings) {
+    /**
+     * Initialise the Node-RED application.
+     * @param {server} httpServer - the HTTP server object to use
+     * @param {Object} userSettings - an object containing the runtime settings
+     * @memberof node-red
+     */
+    init: function(httpServer, userSettings) {
         if (!userSettings) {
             userSettings = httpServer;
             httpServer = null;
@@ -54,27 +63,26 @@ module.exports = {
         }
         redUtil.init(userSettings);
         if (userSettings.httpAdminRoot !== false) {
-            runtime.init(userSettings,api);
-            api.init(httpServer,userSettings,runtime._.storage,runtime);
-
+            runtime.init(userSettings,httpServer,api);
+            api.init(userSettings,httpServer,runtime.storage,runtime);
             apiEnabled = true;
-            server = runtime._.adminApi.server;
-            runtime._.server = runtime._.adminApi.server;
+            server = httpServer;
         } else {
             runtime.init(userSettings);
             apiEnabled = false;
-            if (httpServer){
+            if (httpServer) {
                 server = httpServer;
-                runtime._.server = httpServer;
             } else {
-                server = runtime._.adminApi.server;
-                runtime._.server = runtime._.adminApi.server; // useless at this point, but at least harmless.
+                server = null;
             }
         }
-        adminApp = runtime._.adminApi.adminApp;
-        nodeApp = runtime._.nodeApp;
         return;
     },
+    /**
+     * Start the Node-RED application.
+     * @return {Promise} - resolves when complete
+     * @memberof node-red
+     */
     start: function() {
         return runtime.start().then(function() {
             if (apiEnabled) {
@@ -82,6 +90,11 @@ module.exports = {
             }
         });
     },
+    /**
+     * Stop the Node-RED application.
+     * @return {Promise} - resolves when complete
+     * @memberof node-red
+     */
     stop: function() {
         return runtime.stop().then(function() {
             if (apiEnabled) {
@@ -89,30 +102,37 @@ module.exports = {
             }
         })
     },
-    nodes: runtime._.nodes,
-    log: redUtil.log,
-    settings:runtime._.settings,
-    util: runtime._.util,
-    version: runtime._.version,
-    events: runtime._.events,
-    comms: {
-        publish: function(topic,data,retain) {
-            runtime._.events.emit("comms",{
-                topic: topic,
-                data: data,
-                retain: retain
-            })
-        }
-    },
-    library: {
-        register: function(type) {
-            return runtime._.library.register(null,type);
-        }
-    },
-    auth: api.auth,
 
-    get app() { console.log("Deprecated use of RED.app - use RED.httpAdmin instead"); return runtime._.app },
-    get httpAdmin() { return adminApp },
-    get httpNode() { return nodeApp },
-    get server() { return server }
+    log: redUtil.log,
+    util: redUtil.util,
+
+    get nodes() { console.log("Deprecated use of RED.nodes - refer to API documentation on RED.runtime.nodes"); return runtime._.nodes },
+    get settings() { console.log("Deprecated use of RED.settings - refer to API documentation on RED.runtime.settings"); return runtime._.settings },
+    get version() { console.log("Deprecated use of RED.version - refer to API documentation on RED.runtime.version"); return runtime._.version },
+    get events() { console.log("Deprecated use of RED.events - refer to API documentation on RED.runtime.events"); return runtime.events },
+
+    /**
+     * The express application for the Editor Admin API
+     * @memberof node-red
+     */
+    get httpAdmin() { return api.adminApp },
+
+    /**
+     * The express application for HTTP Nodes
+     * @memberof node-red
+     */
+    get httpNode() { return runtime.httpNode },
+
+    /**
+     * The HTTP Server used by the runtime
+     * @memberof node-red
+     */
+    get server() { return server },
+
+    /**
+     * The runtime api
+     * @see @node-red/runtime
+     * @memberof node-red
+     */
+    runtime: runtime
 };