diff --git a/clusterctl.js b/clusterctl.js
index d02594db..0b5ecc43 100644
--- a/clusterctl.js
+++ b/clusterctl.js
@@ -1,3 +1,7 @@
+/**
+ * Command line interface for controlling a Clusterio cluster
+ * @module
+ */
 const jwt = require("jsonwebtoken");
 const fs = require("fs-extra");
 const yargs = require("yargs");
@@ -16,6 +20,8 @@ const config = require("lib/config");
  *
  * Formats a parsed Factorio output from lib/factorio into a readable
  * colorized output using terminal escape codes that can be printed.
+ *
+ * @private
  */
 function formatOutputColored(output) {
 	let time = "";
@@ -73,6 +79,7 @@ class Command {
  * @param client - link to master server to query instance on.
  * @param instanceName - string with name or id of instance.
  * @returns {number} instance ID.
+ * @private
  */
 async function resolveInstance(client, instanceName) {
 	let instanceId;
@@ -104,6 +111,7 @@ async function resolveInstance(client, instanceName) {
  * @param client - link to master server to query slave on.
  * @param slaveName - string with name or id of slave.
  * @returns {number} slave ID.
+ * @private
  */
 async function resolveSlave(client, slaveName) {
 	let slaveId;
@@ -324,6 +332,7 @@ commands = new Map([...commands.map(command => [command.name, command])]);
 
 /**
  * Connector for control connection to master server
+ * @private
  */
 class ControlConnector extends link.WebSocketClientConnector {
 	constructor(url, reconnectDelay, token) {
diff --git a/docs/jsdoc.json b/docs/jsdoc.json
index 88b1ded8..54216916 100644
--- a/docs/jsdoc.json
+++ b/docs/jsdoc.json
@@ -18,6 +18,7 @@
             "plugins/",
             "routes/",
             "routes.js"
-        ]
+        ],
+        "excludePattern": "node_modules"
     }
 }
diff --git a/lib/config/classes.js b/lib/config/classes.js
index c43ec6be..13196729 100644
--- a/lib/config/classes.js
+++ b/lib/config/classes.js
@@ -1,7 +1,4 @@
-/**
- * @file Configuration classes
- * @author Hornwitser
- */
+// Configuration classes
 "use strict";
 
 const { basicType } = require("lib/helpers");
@@ -12,6 +9,9 @@ const { basicType } = require("lib/helpers");
  *
  * Exception class for when invalid values are attempted to be set on a
  * field.
+ *
+ * @extends Error
+ * @memberof module:lib/config
  */
 class InvalidValue extends Error { };
 
@@ -20,18 +20,26 @@ class InvalidValue extends Error { };
  *
  * Exception class for when a group or field that does not exist is
  * attempted to be accessed.
+ *
+ * @extends Error
+ * @memberof module:lib/config
  */
 class InvalidField extends Error { };
 
 /**
  * Split the given string on the first instance of separator
  *
- * Splits @p string on the first instance of @p separator and returns an
+ * Splits `string` on the first instance of `separator` and returns an
  * array consisting of the string up to the separator and the string
  * after the separator.  Returns an array with the string and an empty
  * string if the separator is not present.
  *
+ * @param {string} separator - Separator to split string by.
+ * @param {string} string - String to split
  * @returns {Array} string split on separator.
+ * @memberof module:lib/config
+ * @private
+ * @inner
  */
 function splitOn(separator, string) {
 	let index = string.indexOf(separator);
@@ -46,6 +54,8 @@ function splitOn(separator, string) {
  *
  * Represents a collection of ConfigGroup instances that can be
  * managed as one.
+ *
+ * @memberof module:lib/config
  */
 class Config {
 	constructor() {
@@ -215,6 +225,8 @@ class Config {
 
 /**
  * Collection of related config entries
+ *
+ * @memberof module:lib/config
  */
 class ConfigGroup {
 	/**
@@ -285,7 +297,7 @@ class ConfigGroup {
 	 * The field must be defined for the config group and the value is
 	 * type checked against the field definition.
 	 *
-	 * @throws {InvalidValue} if value is not allowed for the field.
+	 * @throws {module:lib/config.InvalidValue} if value is not allowed for the field.
 	 */
 	set(name, value) {
 		let def = this.constructor._definitions.get(name);
@@ -553,6 +565,9 @@ class ConfigGroup {
  * Grouping that includes per plugin fields clusterio uses to manage
  * plugins.  This is currently only the enabled field.  It is otherwise
  * identical to the ConfigGroup class.
+ *
+ * @extends module:lib/config.ConfigGroup
+ * @memberof module:lib/config
  */
 class PluginConfigGroup extends ConfigGroup {
 	static _initSubclass() {
diff --git a/lib/config/definitions.js b/lib/config/definitions.js
index 9c1dbc14..c20c61ed 100644
--- a/lib/config/definitions.js
+++ b/lib/config/definitions.js
@@ -1,7 +1,4 @@
-/**
- * @file Core definitions for the configuration system
- * @author Hornwitser
- */
+// Core definitions for the configuration system
 "use strict";
 
 const util = require("util");
@@ -12,6 +9,11 @@ const fs = require("fs-extra");
 const classes = require("./classes");
 
 
+/**
+ * Master config group for {@link module:lib/config.MasterConfig}
+ * @extends module:lib/config.ConfigGroup
+ * @memberof module:lib/config
+ */
 class MasterGroup extends classes.ConfigGroup { }
 MasterGroup.groupName = "master"
 MasterGroup.define({
@@ -103,10 +105,20 @@ MasterGroup.define({
 });
 MasterGroup.finalize();
 
+/**
+ * Master Config class
+ * @extends module:lib/config.Config
+ * @memberof module:lib/config
+ */
 class MasterConfig extends classes.Config { }
 MasterConfig.registerGroup(MasterGroup);
 
 
+/**
+ * Slave config group for {@link module:lib/config.SlaveConfig}
+ * @extends module:lib/config.ConfigGroup
+ * @memberof module:lib/config
+ */
 class SlaveGroup extends classes.ConfigGroup {}
 SlaveGroup.groupName = "slave";
 SlaveGroup.define({
@@ -160,10 +172,20 @@ SlaveGroup.define({
 });
 SlaveGroup.finalize();
 
+/**
+ * Slave Config class
+ * @extends module:lib/config.Config
+ * @memberof module:lib/config
+ */
 class SlaveConfig extends classes.Config { }
 SlaveConfig.registerGroup(SlaveGroup);
 
 
+/**
+ * Instance config group for {@link module:lib/config.InstanceConfig}
+ * @extends module:lib/config.ConfigGroup
+ * @memberof module:lib/config
+ */
 class InstanceGroup extends classes.ConfigGroup { }
 InstanceGroup.groupName = "instance"
 InstanceGroup.define({
@@ -184,6 +206,11 @@ InstanceGroup.define({
 });
 InstanceGroup.finalize();
 
+/**
+ * Factorio config group for {@link module:lib/config.InstanceConfig}
+ * @extends module:lib/config.ConfigGroup
+ * @memberof module:lib/config
+ */
 class FactorioGroup extends classes.ConfigGroup { }
 FactorioGroup.groupName = "factorio";
 FactorioGroup.define({
@@ -221,6 +248,11 @@ FactorioGroup.define({
 });
 FactorioGroup.finalize();
 
+/**
+ * Instance config class
+ * @extends module:lib/config.Config
+ * @memberof module:lib/config
+ */
 class InstanceConfig extends classes.Config { }
 InstanceConfig.registerGroup(InstanceGroup);
 InstanceConfig.registerGroup(FactorioGroup);
@@ -242,6 +274,8 @@ function validateGroup(pluginInfo, groupName) {
 
 /**
  * Registers the config groups for the provided plugin infos
+ *
+ * @memberof module:lib/config
  */
 function registerPluginConfigGroups(pluginInfos) {
 	for (let pluginInfo of pluginInfos) {
@@ -273,6 +307,8 @@ function registerPluginConfigGroups(pluginInfos) {
 
 /**
  * Lock configs from adding more groups and make them usable
+ *
+ * @memberof module:lib/config
  */
 function finalizeConfigs() {
 	MasterConfig.finalize();
@@ -285,6 +321,8 @@ function finalizeConfigs() {
  *
  * Can be passed to yargs.command to implement a config command.  Use
  * handleConfigCommand to do the requested action.
+ *
+ * @memberof module:lib/config
  */
 function configCommand(yargs) {
 	yargs
@@ -300,6 +338,8 @@ function configCommand(yargs) {
  * Handle yargs command
  *
  * Handle the actions that are made available by configCommand.
+ *
+ * @memberof module:lib/config
  */
 async function handleConfigCommand(args, instance, configPath) {
 	let command = args._[1];
diff --git a/lib/config/index.js b/lib/config/index.js
index bbe1c364..f591436e 100644
--- a/lib/config/index.js
+++ b/lib/config/index.js
@@ -1,8 +1,8 @@
 /**
- * @file Configuration System
+ * Configuration System
  * @author Hornwitser
+ * @module lib/config
  */
-
 module.exports = {
 	...require("./classes"),
 	...require("./definitions"),
diff --git a/lib/errors.js b/lib/errors.js
index 19c9d27f..2b9a6bdd 100644
--- a/lib/errors.js
+++ b/lib/errors.js
@@ -3,10 +3,22 @@
  * @module
  */
 
+/**
+ * Thrown by commands when they fail
+ * @static
+ */
 class CommandError extends Error { }
+
+/**
+ * Thrown from requests sent when an error occured handling it
+ * @static
+ */
 class RequestError extends Error { }
 
-// Signal for messages that fail validation
+/**
+ * Signal for messages that fail validation
+ * @static
+ */
 class InvalidMessage extends Error {
 	constructor(msg, errors) {
 		super(msg);
@@ -14,19 +26,34 @@ class InvalidMessage extends Error {
 	}
 }
 
-// Thrown from requests when the session it was sent on was lost.
+/**
+ * Thrown from requests when the session it was sent on was lost
+ * @static
+ */
 class SessionLost extends Error { }
 
-// Thrown when WebSocket authentication failed
+/**
+ * Thrown when WebSocket authentication failed
+ * @static
+ */
 class AuthenticationFailed extends Error { }
 
-// Errror class for known errors occuring during startup
+/**
+ * Errror class for known errors occuring during startup
+ * @static
+ */
 class StartupError extends Error { }
 
-// Errors outside of our control.
+/**
+ * Errors outside of our control
+ * @static
+ */
 class EnvironmentError extends Error { }
 
-// Errors caused by plugins
+/**
+ * Errors caused by plugins
+ * @static
+ */
 class PluginError extends Error {
 	constructor(pluginName, original) {
 		super(`PluginError: ${original.message}`);
diff --git a/lib/factorio/index.js b/lib/factorio/index.js
index 1e03bc70..b99f8803 100644
--- a/lib/factorio/index.js
+++ b/lib/factorio/index.js
@@ -1,3 +1,8 @@
+/**
+ * Library for interfacing with Factorio Servers and saves.
+ * @module lib/factorio
+ * @author Hornwitser
+ */
 module.exports = {
 	...require('lib/factorio/locale'),
 	...require('lib/factorio/patch'),
diff --git a/lib/factorio/locale.js b/lib/factorio/locale.js
index 36ee8a1e..0bc6cef2 100644
--- a/lib/factorio/locale.js
+++ b/lib/factorio/locale.js
@@ -1,7 +1,4 @@
-/**
- * Function for parsing factorio locale from a local factorio install
- */
-
+// Function for parsing factorio locale from a local factorio install
 "use strict";
 const fs = require("fs-extra");
 const path = require("path");
@@ -13,6 +10,7 @@ const ini = require("ini");
  * @param {string} factorioDirectory
  * @param {string} languageCode
  * @param {function} callback
+ * @memberof module:lib/factorio
  */
 async function getLocale(dataDir, languageCode) {
 	if (typeof dataDir !== "string") throw new TypeError("dataDir must be a string");
diff --git a/lib/factorio/patch.js b/lib/factorio/patch.js
index 2d5c1957..e7545be1 100644
--- a/lib/factorio/patch.js
+++ b/lib/factorio/patch.js
@@ -1,7 +1,4 @@
-/**
- * Library for patching Factorio saves with scenario code.
- * @author Hornwitser
- */
+// Library for patching Factorio saves with scenario code.
 
 "use strict";
 const events = require("events");
@@ -31,6 +28,9 @@ const knownScenarios = {
  * contained in.  Throws an error if there are multiple such folders.
  *
  * @returns {string} name of the root folder.
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 function findRoot(zip) {
 	let root = null;
@@ -60,6 +60,9 @@ function findRoot(zip) {
  * Generates control.lua code for loading the Clusterio modules
  *
  * @param {Object} patchInfo - The patch info files's json content
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 function generateLoader(patchInfo) {
 	let lines = [
@@ -107,6 +110,9 @@ function generateLoader(patchInfo) {
  * their dependents.  Throws an error if this is not possible.
  *
  * @param {Array<Object>} modules - Array of modules to reorder
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 function reorderDependencies(modules) {
 	let index = 0;
@@ -202,6 +208,7 @@ function reorderDependencies(modules) {
  *
  * @param {string} savePath - Path to the Factorio save to patch.
  * @param {Array<Object>} modules - Description of the modules to patch.
+ * @memberof module:lib/factorio
  */
 async function patch(savePath, modules) {
 	let zip = await jszip.loadAsync(await fs.readFile(savePath));
diff --git a/lib/factorio/server.js b/lib/factorio/server.js
index 8f7a6540..bf31d557 100644
--- a/lib/factorio/server.js
+++ b/lib/factorio/server.js
@@ -1,9 +1,4 @@
-/**
- * Factorio interfaces
- *
- * @module
- */
-
+// Factorio Server interface
 "use strict";
 const fs = require("fs-extra");
 const child_process = require("child_process");
@@ -20,6 +15,10 @@ const errors = require("lib/errors");
 /**
  * Determines the version of Factorio the datadir is pointing to by
  * reading the changelog.txt in it.
+ *
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 async function getVersion(changelogPath) {
 	let changelog;
@@ -47,6 +46,10 @@ async function getVersion(changelogPath) {
 
 /**
  * Comparison function for sorting Factorio version strings
+ *
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 function versionOrder(a, b) {
 	let aParts = a.split(".").map(s => Number.parseInt(s, 10));
@@ -70,6 +73,10 @@ function versionOrder(a, b) {
  *
  * Searches the given factorio dir for an installation of Factorio of
  * the target version.
+ *
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 async function findVersion(factorioDir, targetVersion) {
 
@@ -125,6 +132,9 @@ async function findVersion(factorioDir, targetVersion) {
  * RFC 6335.
  *
  * @return {number} a number in the range 49152 to 65535.
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 function randomDynamicPort() {
 	const start = 49152;
@@ -141,6 +151,9 @@ function randomDynamicPort() {
  *
  * @param {number} length - the length of the password to generate.
  * @return {string} password of the given length
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 async function generatePassword(length) {
 	function validChar(byte) {
@@ -179,6 +192,10 @@ async function generatePassword(length) {
  * Data is streamed via the data method, and once the stream ends the
  * end method should be called.  This ensures an unterminated line at
  * the end of the stream is passed to the callback.
+ *
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 class LineSplitter {
 
@@ -253,6 +270,9 @@ class LineSplitter {
  * @param {string} source - Passed into the output structure as source
  *
  * @returns {object} - An object with interpeted data.
+ * @memberof module:lib/factorio
+ * @private
+ * @inner
  */
 function parseOutput(line, source) {
 	let output = {
@@ -425,15 +445,17 @@ const outputHeuristics = [
  * stopping and sending commands to the server.  It does not deal with
  * creating or managing servers, or downloading Factorio.
  *
- * This is an events emitter with the following events:
- * stdout - invoked when Factorio outputs a line to stdout
- * stderr - invoked when Factorio outputs a line to stderr
- * output - invoked with parsed output from Factorio
- * rcon-ready - invoked when the RCON client has connected
- * game-ready - invoked when the server is finished starting up
- * autosave-start - invoked when the server starts an autosave
- * autosave-fnished - invoked when the autosave finished
- * exit - invoked when the sterver has exited
+ * This is an EventEmitter with the following events:
+ * - stdout - invoked when Factorio outputs a line to stdout
+ * - stderr - invoked when Factorio outputs a line to stderr
+ * - output - invoked with parsed output from Factorio
+ * - rcon-ready - invoked when the RCON client has connected
+ * - game-ready - invoked when the server is finished starting up
+ * - autosave-start - invoked when the server starts an autosave
+ * - autosave-fnished - invoked when the autosave finished
+ * - exit - invoked when the sterver has exited
+ * @extends events.EventEmitter
+ * @memberof module:lib/factorio
  */
 class FactorioServer extends events.EventEmitter {
 	/**
@@ -442,6 +464,12 @@ class FactorioServer extends events.EventEmitter {
 	 * @param {string} factorioDir - Directory of the Factorio install(s).
 	 * @param {string} writeDir - Directory to write runtime data to.
 	 * @param {object} options - Optional parameters.
+	 * @param {string} options.version -
+	 *     Version of Factorio to use.  Can also be the string "latest" to
+	 *     use the latest version found in `factorioDir`.
+	 * @param {number} options.gamePort - UDP port to host game on.
+	 * @param {number} options.rconPort - TCP port to use for RCON.
+	 * @param {string} options.rconPassword - Password use for RCON.
 	 */
 	constructor(factorioDir, writeDir, options) {
 		super();
@@ -454,8 +482,11 @@ class FactorioServer extends events.EventEmitter {
 		this._dataDir = null;
 
 		this._targetVersion = options.version || "latest";
+		/** UDP port used for hosting the Factorio game server on */
 		this.gamePort = options.gamePort || randomDynamicPort();
+		/** TCP port used for RCON on the Factorio game server */
 		this.rconPort = options.rconPort || randomDynamicPort();
+		/** Password used for RCON on the Factorio game server */
 		this.rconPassword = options.rconPassword;
 		this._state = "new";
 		this._server = null;
@@ -603,6 +634,7 @@ class FactorioServer extends events.EventEmitter {
 	 * Initialize class instance
 	 *
 	 * Must be called before instances of this class can be used.
+	 * @throws {Error} if the requested version of Factorio was not found.
 	 */
 	async init() {
 		this._check(["new"]);
@@ -612,7 +644,9 @@ class FactorioServer extends events.EventEmitter {
 	}
 
 	/**
-	 * The version of Factorio that was detected
+	 * The version of Factorio in use.  This will be the actual version if
+	 * "latest" (the default) was specified as `factorioVersion` to the
+	 * constructor.
 	 */
 	get version() {
 		return this._version;
diff --git a/lib/fileOps/fileOps.js b/lib/fileOps/fileOps.js
index 251991a3..ed42b794 100644
--- a/lib/fileOps/fileOps.js
+++ b/lib/fileOps/fileOps.js
@@ -1,3 +1,6 @@
+/**
+ * @module lib/fileOps
+ */
 const fs = require("fs-extra");
 const path = require("path");
 
diff --git a/lib/hash.js b/lib/hash.js
index 9cf9c4bf..9bb694ed 100644
--- a/lib/hash.js
+++ b/lib/hash.js
@@ -1,3 +1,7 @@
+/**
+ * Hashing functions
+ * @module
+ */
 const crypto = require('crypto');
 const fs = require('fs');
 
@@ -6,6 +10,7 @@ const fs = require('fs');
  * Returns a promise that resolves to the SHA1 hash of the stream given
  *
  * @param stream - Node stream of the content to hash.
+ * @returns {Promise<string>} hash of the stream.
  */
 function hashStream(stream) {
 	return new Promise(function(resolve, reject) {
@@ -28,6 +33,7 @@ function hashStream(stream) {
  * Returns a promise that resolves to the SHA1 hash of the file given by path
  *
  * @param {string} path - Path to the file to hash.
+ * @returns {Promise<string>} hash of the file given.
  */
 function hashFile(path) {
 	return hashStream(fs.createReadStream(path));
diff --git a/lib/link/connectors.js b/lib/link/connectors.js
index d7afe5fc..1b6b4d78 100644
--- a/lib/link/connectors.js
+++ b/lib/link/connectors.js
@@ -1,3 +1,4 @@
+// Connection adapters for Links
 "use strict";
 const events = require("events");
 const WebSocket = require("ws");
@@ -6,6 +7,12 @@ const schema = require("lib/schema");
 const errors = require("lib/errors");
 
 
+/**
+ * Base connector for links
+ *
+ * @extends events.EventEmitter
+ * @memberof module:lib/link
+ */
 class WebSocketBaseConnector extends events.EventEmitter {
 	constructor() {
 		super();
@@ -112,6 +119,9 @@ class WebSocketBaseConnector extends events.EventEmitter {
 
 /**
  * Connector for master server clients
+ *
+ * @extends module:lib/link.WebSocketBaseConnector
+ * @memberof module:lib/link
  */
 class WebSocketClientConnector extends WebSocketBaseConnector {
 	constructor(url, reconnectDelay) {
@@ -397,6 +407,12 @@ class WebSocketClientConnector extends WebSocketBaseConnector {
 	}
 }
 
+/**
+ * Connector for in-memory local links
+ *
+ * @extends events.EventEmitter
+ * @memberof module:lib/link
+ */
 class VirtualConnector extends events.EventEmitter {
 	constructor() {
 		super();
diff --git a/lib/link/index.js b/lib/link/index.js
index 132ff5d0..e5c18c5f 100644
--- a/lib/link/index.js
+++ b/lib/link/index.js
@@ -1,3 +1,8 @@
+/**
+ * Library for message based communication between nodes
+ * @module lib/link
+ * @author Hornwitser
+ */
 module.exports = {
 	...require('lib/link/link'),
 	...require('lib/link/messages'),
diff --git a/lib/link/link.js b/lib/link/link.js
index d36d8b56..347efef4 100644
--- a/lib/link/link.js
+++ b/lib/link/link.js
@@ -1,3 +1,4 @@
+// Implementation of Link class
 "use strict";
 
 const schema = require("lib/schema");
@@ -15,6 +16,8 @@ const messages = require("lib/link/messages");
 
 /**
  * Common interface for server and client connections
+ *
+ * @memberof module:lib/link
  */
 class Link {
 	constructor(source, target, connector) {
@@ -59,7 +62,7 @@ class Link {
 	 * Validates and invokes the handler and/or waiters for a message that has
 	 * been received.  An unhandled message is considered to be an error.
 	 *
-	 * @throws {InvalidMessage}
+	 * @throws {module:lib/errors.InvalidMessage}
 	 *     if validation failed, is missing, the message is invalid, or no
 	 *     handlers/waiters were invoked to handle the message.
 	 */
diff --git a/lib/link/messages.js b/lib/link/messages.js
index 365bfa6a..8edf569e 100644
--- a/lib/link/messages.js
+++ b/lib/link/messages.js
@@ -1,3 +1,4 @@
+// Message definitions for links
 "use strict";
 const schema = require("lib/schema");
 const errors = require("lib/errors");
@@ -7,6 +8,8 @@ const errors = require("lib/errors");
  *
  * A request-response message that can be innitated by either party of the
  * link.
+ *
+ * @memberof module:lib/link
  */
 class Request {
 
@@ -353,6 +356,8 @@ messages.getMetrics = new Request({
  *
  * A one way message without any response or recipt confirmation that
  * can be innitiated by either party of the link.
+ *
+ * @memberof module:lib/link
  */
 class Event {
 
@@ -555,6 +560,8 @@ messages.instanceOutput = new Event({
  * to the link.  The handler used for the messageis looked up on the
  * link instance as the concatenation of the name of the message, the
  * name of message class, and 'Handler'.
+ *
+ * @memberof module:lib/link
  */
 function attachAllMessages(link) {
 	for (let [name, message] of Object.entries(messages)) {
diff --git a/lib/luaTools.js b/lib/luaTools.js
index 8165beb5..7566e03e 100644
--- a/lib/luaTools.js
+++ b/lib/luaTools.js
@@ -1,3 +1,8 @@
+/**
+ * Utilities for dealing with Lua
+ * @module
+ */
+
 /**
  * Escapes a string for inclusion into a lua string
  */
diff --git a/lib/plugin.js b/lib/plugin.js
index 41661db3..7dd6a3ad 100644
--- a/lib/plugin.js
+++ b/lib/plugin.js
@@ -11,6 +11,7 @@ const errors = require("lib/errors");
 
 /**
  * Base class for instance plugins
+ * @static
  */
 class BaseInstancePlugin {
 	constructor(info, instance, slave) {
@@ -21,7 +22,7 @@ class BaseInstancePlugin {
 
 		/**
 		 * Instance the plugin started for
-		 * @type {Instance}
+		 * @type {module:slave~Instance}
 		 */
 		this.instance = instance;
 
@@ -31,7 +32,7 @@ class BaseInstancePlugin {
 		 * With the exepction of accessing the slave's config you should
 		 * avoid ineracting with the slave object directly.
 		 *
-		 * @type {Slave}
+		 * @type {module:slave~Slave}
 		 */
 		this.slave = slave;
 	}
@@ -95,6 +96,10 @@ class BaseInstancePlugin {
 	async onOutput(output) { }
 }
 
+/**
+ * Base class for master plugins
+ * @static
+ */
 class BaseMasterPlugin {
 	constructor(info, master, metrics) {
 		this.info = info;
@@ -138,6 +143,7 @@ class BaseMasterPlugin {
  * function be called again.
  *
  * @returns {Map<string, Object>} mapping of plugin name to info module.
+ * @static
  */
 async function loadPluginInfos(baseDir) {
 	let plugins = [];
@@ -167,6 +173,16 @@ async function loadPluginInfos(baseDir) {
 	return plugins;
 }
 
+/**
+ * Attach plugin messages
+ *
+ * Attaches all messages defined in the `.message` property of the
+ * `pluginInfo` passed with handlers taken from `pluin`.
+ *
+ * @param {module:lib/link.Link} link - Link to attach handlers to.
+ * @param {object} pluginInfo - Plugin info object.
+ * @param plugin - The instance of the plugin to use handlers from.
+ */
 function attachPluginMessages(link, pluginInfo, plugin) {
 	let messageDefinitions = pluginInfo.messages || [];
 	for (let [name, messageFormat] of Object.entries(messageDefinitions)) {
diff --git a/lib/schema.js b/lib/schema.js
index 07e649f6..84fc6de0 100644
--- a/lib/schema.js
+++ b/lib/schema.js
@@ -1,3 +1,7 @@
+/**
+ * JSON schemas used for validating link messages
+ * @module
+ */
 const ajv = new (require('ajv'))({
 	verbose: true,
 	format: "full",
@@ -24,8 +28,20 @@ const messageSchema = {
 	},
 };
 
+/**
+ * Validator for message schemas
+ * @function
+ * @param {Object} obj - Object to validate
+ * @returns {boolean} True if object passed validation.
+ */
 const message = ajv.compile(messageSchema);
 
+/**
+ * Validator for heartbeat messages
+ * @function
+ * @param {Object} obj - Object to validate
+ * @returns {boolean} True if object passed validation.
+ */
 const heartbeat = ajv.compile({
 	$schema: "http://json-schema.org/draft-07/schema#",
 	title: "Heartbeat",
@@ -47,6 +63,12 @@ const heartbeat = ajv.compile({
 	},
 });
 
+/**
+ * Validator for server sent part of handshake
+ * @function
+ * @param {Object} obj - Object to validate
+ * @returns {boolean} True if object passed validation.
+ */
 const serverHandshake = ajv.compile({
 	$schema: "http://json-schema.org/draft-07/schema#",
 	title: "Server Handshake",
@@ -104,6 +126,12 @@ const serverHandshake = ajv.compile({
 	],
 });
 
+/**
+ * Validator for client sent part of handshake
+ * @function
+ * @param {Object} obj - Object to validate
+ * @returns {boolean} True if object passed validation.
+ */
 const clientHandshake = ajv.compile({
 	$schema: "http://json-schema.org/draft-07/schema#",
 	title: "Client Message",
@@ -162,6 +190,12 @@ const clientHandshake = ajv.compile({
 
 
 module.exports = {
+	/**
+	 * Compile JSON schema into validator
+	 * @function
+	 * @param {Object} schema - JSON schema to create validator for.
+	 * @returns {Function} Validator for the schema.
+	 */
 	compile: ajv.compile.bind(ajv),
 
 	message,
diff --git a/master.js b/master.js
index f2dba036..b6885823 100644
--- a/master.js
+++ b/master.js
@@ -1,13 +1,16 @@
 /**
-Clusterio master server. Facilitates communication between slaves through
-a webserver, storing data related to slaves like production graphs.
-
-@module
-@author Danielv123
-
-@example
-node master
-*/
+ * Clusterio master server
+ *
+ * Facilitates communication between slaves and control of the cluster
+ * through WebSocet connections, and hosts a webserver for browser
+ * interfaces and Prometheus statistics export.  It is remotely controlled
+ * by {@link module:clusterctl}.
+ *
+ * @module
+ * @author Danielv123, Hornwitser
+ * @example
+ * node master run
+ */
 
 // Attempt updating
 // const updater = require("./updater");
@@ -345,6 +348,11 @@ app.get("/api/getFactorioLocale", function(req,res){
 	}
 });
 
+/**
+ * Base class for master server connections
+ *
+ * @extends module:lib/link.Link
+ */
 class BaseConnection extends link.Link {
 	constructor(target, connector) {
 		super('master', target, connector);
@@ -574,6 +582,11 @@ class ControlConnection extends BaseConnection {
 }
 
 var slaveConnections = new Map();
+/**
+ * Represents the connection to a slave
+ *
+ * @extends module:master~BaseConnection
+ */
 class SlaveConnection extends BaseConnection {
 	constructor(registerData, connector) {
 		super('slave', connector);
@@ -647,7 +660,8 @@ const wss = new WebSocket.Server({
  *
  * @param value - value to test.
  * @returns {Boolean}
- *     true if value is an integer between -2**31 and 2**31-1.
+ *     true if value is an integer between -2<sup>31</sup> and
+ *     2<sup>31</sup>-1.
  */
 function isInteger(value) {
 	return value | 0 === value;
@@ -656,6 +670,8 @@ function isInteger(value) {
 
 /**
  * Connector for master server connections
+ *
+ * @extends module:lib/link.WebSocketBaseConnector
  */
 class WebSocketServerConnector extends link.WebSocketBaseConnector {
 	constructor(socket, sessionId) {
diff --git a/plugins/global_chat/instance.js b/plugins/global_chat/instance.js
index e44ed210..2674a03d 100644
--- a/plugins/global_chat/instance.js
+++ b/plugins/global_chat/instance.js
@@ -1,3 +1,6 @@
+/**
+ * @module
+ */
 const plugin = require("lib/plugin");
 const luaTools = require("lib/luaTools");
 
diff --git a/slave.js b/slave.js
index 78041eb1..716d092e 100644
--- a/slave.js
+++ b/slave.js
@@ -1,3 +1,15 @@
+/**
+ * Clusterio slave
+ *
+ * Connects to the master server and hosts Factorio servers that can
+ * communicate with the cluster.  It is remotely controlled by {@link
+ * module:master}.
+ *
+ * @module
+ * @author Danielv123, Hornwitser
+ * @example
+ * node slave run
+ */
 const fs = require('fs-extra');
 const path = require('path');
 const yargs = require("yargs");