changed the config to omit the keys, those are loaded in loader.user.js

Author: rlemon

loader.user.js

@@ -2,11 +2,20 @@
 // @name ChatBot auto-loader
 // @author Zirak
 // @namespace ZirakInSpace
-// @version 0.1
+// @version 0.2
 // @description Loads the bot when you visit a room
 // @include /http://chat\.stack(overflow|exchange)\.com/rooms/\d+/
 // ==/UserScript==
 
 var s = document.createElement( 'script' );
+s.onload = runConfigs;
 s.src = 'https://rawgit.com/Zirak/SO-ChatBot/master/master.js';
 document.head.appendChild( s );
+
+function runConfigs() {
+	var config = bot.config;
+	config.weatherKey = '';
+	config.githubToken = '';
+	bot.memory.set('config', config);
+	bot.memory.save();
+}

master.js

@@ -2109,13 +2109,13 @@ module.exports = function (bot) {
             pattern: '!!',
             welcomeMessage: welcomeFmt.supplant(rulesLink),
 
-            // visit OpenWeatherMap site to obtain a key.
-            // the sample key no longer works.
-            weatherKey: 'sample',
+            // these must be set for the weather
+            // command and backup command respectivly.
+            // I've removed the sample keys so I can easily
+            // change them with the bot loader script.
 
-            // visit github to obtain a key
-            // no public keys work.
-            githubToken: 'sample'
+            //weatherKey: '',
+            //githubToken: ''
         },
         bot.memory.get('config', {})
     );

master.min.js

@@ -12,13 +12,13 @@ module.exports = function (bot) {
             pattern: '!!',
             welcomeMessage: welcomeFmt.supplant(rulesLink),
 
-            // visit OpenWeatherMap site to obtain a key.
-            // the sample key no longer works.
-            weatherKey: 'sample',
+            // these must be set for the weather
+            // command and backup command respectivly.
+            // I've removed the sample keys so I can easily
+            // change them with the bot loader script.
 
-            // visit github to obtain a key
-            // no public keys work.
-            githubToken: 'sample'
+            //weatherKey: '',
+            //githubToken: ''
         },
         bot.memory.get('config', {})
     );