diff --git a/lib/core/config.js b/lib/core/config.js
index a71a72ee..cb1003ab 100644
--- a/lib/core/config.js
+++ b/lib/core/config.js
@@ -227,7 +227,11 @@ Config.prototype.loadEmbarkConfigFile = function() {
 Config.prototype.loadPipelineConfigFile = function() {
   var assets = this.embarkConfig.app;
   for(var targetFile in assets) {
-    this.assetFiles[targetFile] = this.loadFiles(assets[targetFile]);
+    if (typeof(assets[targetFile]) === 'string' || (Array.isArray(assets[targetFile]) && (assets[targetFile].length === 1))) {
+      this.assetFiles[targetFile] = this.loadFile(assets[targetFile]);
+    } else {
+      this.assetFiles[targetFile] = this.loadFiles(assets[targetFile]);
+    }
   }
 };
 
@@ -245,6 +249,101 @@ Config.prototype.loadChainTrackerFile = function() {
   this.chainTracker = chainTracker;
 };
 
+Config.prototype.loadFile = function(files) {
+  var self = this;
+  var originalFiles = utils.filesMatchingPattern(files);
+  var readFiles = [];
+
+  // get plugins
+  var filesFromPlugins = [];
+
+  var filePlugins = self.plugins.getPluginsFor('pipelineFiles');
+
+  if (filePlugins.length > 0) {
+    filePlugins.forEach(function(plugin) {
+      try {
+        var fileObjects = plugin.runFilePipeline();
+        for (var i=0; i < fileObjects.length; i++) {
+          var fileObject = fileObjects[i];
+          filesFromPlugins.push(fileObject);
+        }
+      }
+      catch(err) {
+        self.logger.error(err.message);
+      }
+    });
+  }
+
+  filesFromPlugins.filter(function(file) {
+    if (utils.fileMatchesPattern(files, file.intendedPath)) {
+      readFiles.push(file);
+    }
+  });
+
+  // get user files
+  originalFiles.filter(function(file) {
+    return file.indexOf('.') >= 0;
+  }).filter(function(file) {
+    if (file === 'embark.js') {
+      return;
+    } else if (file.indexOf("web3-") === 0) {
+      return;
+    } else if (file.indexOf("web3") === 0) {
+      return;
+    //} else if (file === 'abi.js') {
+    //  readFiles.push({filename: file, content: "", path: file});
+    } else {
+
+      if (file.indexOf('.js') >= 0) {
+      //if (file.indexOf('.js') >= 0) {
+        readFiles.push(new File({filename: file, type: "custom", path: file, resolver: function(callback) {
+          console.log("---");
+          console.log(fs.dappPath());
+          console.log(file);
+          console.log("---");
+          webpack({
+            entry: utils.joinPath(fs.dappPath(), file),
+            output: {
+              //libraryTarget: 'umd',
+              path: utils.joinPath(fs.dappPath(), '.embark'),
+              //filename: 'my-first-webpack.bundle.js'
+              filename: file
+            },
+            externals: function(context, request, callback) {
+              if (request == "MyLib") {
+                console.log("MyLib Detected!");
+                return callback(null, "{foo: 'hello'}");
+              }
+              callback();
+            },
+            module: {
+              rules: [
+                {
+                  test: /\.css$/,
+                  use: [
+                    { loader: "style-loader" },
+                    { loader: "css-loader" }
+                  ]
+                }
+              ]
+            }
+          }).run((err, stats) => {
+            console.log(err, stats);
+            //return callback(fs.readFileSync('./.embark/my-first-webpack.bundle.js').toString());
+            return callback(fs.readFileSync('./.embark/' + file).toString());
+          });
+        }}));
+      } else {
+        readFiles.push(new File({filename: file, type: "dapp_file", path: file}));
+      }
+
+    }
+
+  });
+
+  return readFiles;
+};
+
 Config.prototype.loadFiles = function(files) {
   var self = this;
   var originalFiles = utils.filesMatchingPattern(files);
@@ -335,55 +434,7 @@ Config.prototype.loadFiles = function(files) {
     //} else if (file === 'abi.js') {
     //  readFiles.push({filename: file, content: "", path: file});
     } else {
-
-      if (file.indexOf('index.js') >= 0) {
-      //if (file.indexOf('.js') >= 0) {
-        readFiles.push(new File({filename: file, type: "custom", path: file, resolver: function(callback) {
-          console.log("---");
-          console.log(fs.dappPath());
-          console.log(file);
-          console.log("---");
-          webpack({
-            entry: utils.joinPath(fs.dappPath(), file),
-            output: {
-              //libraryTarget: 'umd',
-              path: utils.joinPath(fs.dappPath(), '.embark'),
-              //filename: 'my-first-webpack.bundle.js'
-              filename: file
-            },
-            externals: function(context, request, callback) {
-              if (request == "MyLib") {
-                console.log("MyLib Detected!");
-                return callback(null, "{foo: 'hello'}");
-              }
-              callback();
-            },
-            module: {
-              rules: [
-                {
-                  test: /\.css$/,
-                  use: [
-                    { loader: "style-loader" },
-                    { loader: "css-loader" }
-                  ]
-                }
-              ]
-            }
-          }).run((err, stats) => {
-            console.log(err, stats);
-            //return callback(fs.readFileSync('./.embark/my-first-webpack.bundle.js').toString());
-            return callback(fs.readFileSync('./.embark/' + file).toString());
-          });
-        }}));
-      } else {
-        readFiles.push(new File({filename: file, type: "dapp_file", path: file}));
-      }
-
-      //if (file.indexOf('.') >= 0)  {
-      //  readFiles.push(new File({filename: file, type: "dapp_file", path: file}));
-      //} else if (file[0] === '$') {
-      //  //readFiles.push(new File({filename: file, type: 'embark_internal', path: file}));
-      //}
+      readFiles.push(new File({filename: file, type: "dapp_file", path: file}));
     }
   });
 
diff --git a/test_app/app/js/index.js b/test_app/app/js/index.js
index caa255cb..cbf16091 100644
--- a/test_app/app/js/index.js
+++ b/test_app/app/js/index.js
@@ -1,12 +1,5 @@
 /*globals $, SimpleStorage, document*/
 
-import Test2 from 'MyLib';
-
-import test3 from './foo';
-import './foo.css';
-
-window.test_3 = test3;
-
 var addToLog = function(id, txt) {
   $(id + " .logs").append("<br>" + txt);
 };
@@ -15,9 +8,6 @@ var addToLog = function(id, txt) {
 // Blockchain example
 // ===========================
 $(document).ready(function() {
-  console.log([1,2,3].map(v => v + 1));
-  alert('hello');
-  window.test_2 = Test2;
 
   $("#blockchain button.set").click(function() {
     var value = parseInt($("#blockchain input.text").val(), 10);
diff --git a/test_app/app/js/new_index.js b/test_app/app/js/new_index.js
new file mode 100644
index 00000000..64fe318d
--- /dev/null
+++ b/test_app/app/js/new_index.js
@@ -0,0 +1,166 @@
+/*globals $, SimpleStorage, document*/
+
+import $ from './_vendor/jquery.min';
+//import EmbarkJS from 'Embark/EmbarkJS';
+
+import Test2 from 'MyLib';
+
+import test3 from './foo';
+import './foo.css';
+
+window.test_3 = test3;
+
+var addToLog = function(id, txt) {
+  $(id + " .logs").append("<br>" + txt);
+};
+
+// ===========================
+// Blockchain example
+// ===========================
+$(document).ready(function() {
+  console.log([1,2,3].map(v => v + 1));
+  alert('hello');
+  window.test_2 = Test2;
+
+  $("#blockchain button.set").click(function() {
+    var value = parseInt($("#blockchain input.text").val(), 10);
+
+    // If web3.js 1.0 is being used
+    if (EmbarkJS.isNewWeb3()) {
+      SimpleStorage.methods.set(value).send({from: web3.eth.defaultAccount});
+      addToLog("#blockchain", "SimpleStorage.methods.set(value).send({from: web3.eth.defaultAccount})");
+    } else {
+      SimpleStorage.set(value);
+      addToLog("#blockchain", "SimpleStorage.set(" + value + ")");
+    }
+
+  });
+
+  $("#blockchain button.get").click(function() {
+    // If web3.js 1.0 is being used
+    if (EmbarkJS.isNewWeb3()) {
+      SimpleStorage.methods.get().call(function(err, value) {
+        $("#blockchain .value").html(value);
+      });
+      addToLog("#blockchain", "SimpleStorage.methods.get(console.log)");
+    } else {
+      SimpleStorage.get().then(function(value) {
+        $("#blockchain .value").html(value.toNumber());
+      });
+      addToLog("#blockchain", "SimpleStorage.get()");
+    }
+  });
+
+});
+
+// ===========================
+// Storage (IPFS) example
+// ===========================
+$(document).ready(function() {
+  // automatic set if config/storage.json has "enabled": true and "provider": "ipfs"
+  //EmbarkJS.Storage.setProvider('ipfs',{server: 'localhost', port: '5001'});
+
+  $("#storage .error").hide();
+  EmbarkJS.Storage.ipfsConnection.ping()
+    .then(function(){
+        $("#status-storage").addClass('status-online');
+        $("#storage-controls").show();
+    })
+    .catch(function(err) {
+      if(err){
+        console.log("IPFS Connection Error => " + err.message);
+        $("#storage .error").show();
+        $("#status-storage").addClass('status-offline');
+        $("#storage-controls").hide();
+      }
+    });
+
+  $("#storage button.setIpfsText").click(function() {
+    var value = $("#storage input.ipfsText").val();
+    EmbarkJS.Storage.saveText(value).then(function(hash) {
+      $("span.textHash").html(hash);
+      $("input.textHash").val(hash);
+      addToLog("#storage", "EmbarkJS.Storage.saveText('" + value + "').then(function(hash) { })");
+    })
+    .catch(function(err) {
+      if(err){
+        console.log("IPFS saveText Error => " + err.message);
+      }
+    });
+  });
+
+  $("#storage button.loadIpfsHash").click(function() {
+    var value = $("#storage input.textHash").val();
+    EmbarkJS.Storage.get(value).then(function(content) {
+      $("span.ipfsText").html(content);
+      addToLog("#storage", "EmbarkJS.Storage.get('" + value + "').then(function(content) { })");
+    })
+    .catch(function(err) {
+      if(err){
+        console.log("IPFS get Error => " + err.message);
+      }
+    });
+  });
+
+  $("#storage button.uploadFile").click(function() {
+    var input = $("#storage input[type=file]");
+    EmbarkJS.Storage.uploadFile(input).then(function(hash) {
+      $("span.fileIpfsHash").html(hash);
+      $("input.fileIpfsHash").val(hash);
+      addToLog("#storage", "EmbarkJS.Storage.uploadFile($('input[type=file]')).then(function(hash) { })");
+    })
+    .catch(function(err) {
+      if(err){
+        console.log("IPFS uploadFile Error => " + err.message);
+      }
+    });
+  });
+
+  $("#storage button.loadIpfsFile").click(function() {
+    var hash = $("#storage input.fileIpfsHash").val();
+    var url = EmbarkJS.Storage.getUrl(hash);
+    var link = '<a href="' + url + '" target="_blank">' + url + '</a>';
+    $("span.ipfsFileUrl").html(link);
+    $(".ipfsImage").attr('src', url);
+    addToLog("#storage", "EmbarkJS.Storage.getUrl('" + hash + "')");
+  });
+
+});
+
+// ===========================
+// Communication (Whisper) example
+// ===========================
+$(document).ready(function() {
+
+  $("#communication .error").hide();
+  $("#communication .errorVersion").hide();
+  if (EmbarkJS.Messages.providerName === 'whisper') {
+    EmbarkJS.Messages.getWhisperVersion(function(err, version) {
+      if (err) {
+        $("#communication .error").show();
+        $("#communication-controls").hide();
+        $("#status-communication").addClass('status-offline');
+      } else {
+        EmbarkJS.Messages.setProvider('whisper');
+        $("#status-communication").addClass('status-online');
+      }
+    });
+  }
+
+  $("#communication button.listenToChannel").click(function() {
+    var channel = $("#communication .listen input.channel").val();
+    $("#communication #subscribeList").append("<br> subscribed to " + channel + " now try sending a message");
+    EmbarkJS.Messages.listenTo({topic: [channel]}).then(function(message) {
+      $("#communication #messagesList").append("<br> channel: " + channel + " message: " + message);
+    });
+    addToLog("#communication", "EmbarkJS.Messages.listenTo({topic: ['" + channel + "']}).then(function(message) {})");
+  });
+
+  $("#communication button.sendMessage").click(function() {
+    var channel = $("#communication .send input.channel").val();
+    var message = $("#communication .send input.message").val();
+    EmbarkJS.Messages.sendMessage({topic: channel, data: message});
+    addToLog("#communication", "EmbarkJS.Messages.sendMessage({topic: '" + channel + "', data: '" + message + "'})");
+  });
+
+});
diff --git a/test_app/app/new_index.html b/test_app/app/new_index.html
new file mode 100644
index 00000000..1bf3a925
--- /dev/null
+++ b/test_app/app/new_index.html
@@ -0,0 +1,107 @@
+<html>
+  <head>
+    <title>Embark - SimpleStorage Demo</title>
+    <link rel="stylesheet" href="css/app.css">
+    <script src="js/new_app.js"></script>
+  </head>
+  <body class="container">
+    <h3>Embark - Usage Example</h3>
+
+    <ul class="nav nav-tabs" role="tablist" id="myTabs">
+      <li role="presentation" class="active"><a href="#blockchain" aria-controls="blockchain" role="tab" data-toggle="tab">Blockchain</a></li>
+      <li role="presentation"><a href="#storage" aria-controls="storage" role="tab" data-toggle="tab">Decentralized Storage (IPFS)<span class="pull-right" id="status-storage"></a></li>
+      <li role="presentation"><a href="#communication" aria-controls="communication" role="tab" data-toggle="tab">P2P communication (Whisper/Orbit)<span class="pull-right" id="status-communication"></span></a></li>
+    </ul>
+
+    <div class="tab-content">
+      <div role="tabpanel" class="tab-pane active" id="blockchain">
+        <h3> 1. Set the value in the blockchain</h3>
+        <div class="form-group form-inline">
+          <input type="text" class="text form-control" value="10">
+          <button class="set btn btn-primary">Set Value</button>
+          <p>Once you set the value, the transaction will need to be mined and then the value will be updated on the blockchain.</p>
+        </div>
+
+        <h3> 2. Get the current value</h3>
+        <div class="form-group">
+          <div>
+            current value is <span class="value"></span>
+          </div>
+          <button class="get btn btn-primary">Get Value</button>
+          <p>Click the button to get the current value. The initial value is 100.</p>
+        </div>
+
+        <h3> 3. Contract Calls </h3>
+        <p>Javascript calls being made: </p>
+        <div class="logs">
+        </div>
+      </div>
+      <div role="tabpanel" class="tab-pane" id="storage">
+        <div class="error alert alert-danger" role="alert">The node you are using does not support IPFS. Please ensure <a href="https://github.com/ipfs/js-ipfs-api#cors" target="_blank">CORS</a> is setup for the IPFS node.</div>
+        <div id="storage-controls">
+
+        <h3>Save text to IPFS</h3>
+        <div class="form-group form-inline">
+          <input type="text" class="ipfsText text form-control" value="hello world!">
+          <button class="setIpfsText btn btn-primary">Save</button>
+          <p>generated Hash: <span class="textHash"></span></p>
+        </div>
+
+        <h3>Load text from IPFS given an hash</h3>
+        <div class="form-group form-inline">
+          <input type="text" class="textHash text form-control" size="60">
+          <button class="loadIpfsHash set btn btn-primary">Load</button>
+          <p>result: <span class="ipfsText"></span></p>
+        </div>
+
+        <h3>upload file to ipfs</h3>
+        <div class="form-group form-inline">
+          <input type="file" class="form-control">
+          <button class="uploadFile set btn btn-primary">upload</button>
+          <p>generated hash: <span class="fileIpfsHash"></span></p>
+        </div>
+
+        <h3>Get file or image from ipfs</h3>
+        <div class="form-group form-inline">
+          <input type="text" class="fileIpfsHash form-control" size="60">
+          <button class="loadIpfsFile set btn btn-primary">Load</button>
+          <p>file available at: <span class="ipfsFileUrl"></span></p>
+          <p><img class="ipfsImage" src=""></p>
+        </div>
+
+        <p>Javascript calls being made: </p>
+        <div class="logs">
+          <br> EmbarkJS.Storage.setProvider('ipfs',{server: 'localhost', port: '5001'})
+        </div>
+      </div>
+      </div>
+      <div role="tabpanel" class="tab-pane" id="communication">
+        <div class="error alert alert-danger" role="alert">The node you are using does not support Whisper</div>
+        <div class="errorVersion alert alert-danger" role="alert">The node uses an unsupported version of Whisper</div>
+        <div id="communication-controls">
+        <h3>Listen To channel</h3>
+        <div class="form-group form-inline listen">
+          <input type="text" class="channel text form-control" placeholder="channel">
+          <button class="listenToChannel set btn btn-primary">Start Listening</button>
+          <div id="subscribeList"></div>
+          <p>messages received:<p>
+          <div id="messagesList"></div>
+        </div>
+
+        <h3>Send Message</h3>
+        <div class="form-group form-inline send">
+          <input type="text" class="channel text form-control" placeholder="channel">
+          <input type="text" class="message text form-control" placeholder="message">
+          <button class="sendMessage set btn btn-primary">Send Message</button>
+        </div>
+
+        <p>Javascript calls being made: </p>
+        <div class="logs">
+          <br> EmbarkJS.Messages.setProvider('whisper')
+        </div>
+      </div>
+      </div>
+    </div>
+
+  </body>
+</html>
diff --git a/test_app/embark.json b/test_app/embark.json
index 2f08464d..57b46ad2 100644
--- a/test_app/embark.json
+++ b/test_app/embark.json
@@ -4,12 +4,14 @@
     "js/webpack_test.js": "app/js/index.js",
     "css/app.css": ["app/css/**"],
     "images/": ["app/images/**"],
-    "js/app.js": ["embark.js", "app/js/_vendor/jquery.min.js", "app/js/_vendor/bootstrap.min.js", "app/js/**", "!app/js/test.js", "!app/js/foo.js", "!app/js/foo.css"],
+    "js/app.js": ["embark.js", "app/js/_vendor/jquery.min.js", "app/js/_vendor/bootstrap.min.js", "app/js/**", "!app/js/test.js", "!app/js/foo.js", "!app/js/foo.css", "!app/js/new_index.js"],
+    "js/new_app.js": ["app/js/new_index.js"],
     "js/embark.js": ["embark.js"],
     "js/abi.js": "abi.js",
     "js/test.js": ["embark.js", "app/js/_vendor/jquery.min.js", "app/js/_vendor/async.min.js", "app/js/test.js"],
     "js/mytoken.js": ["$MyToken", "app/js/token_test.js"],
     "index.html": "app/index.html",
+    "new_index.html": "app/new_index.html",
     "test.html": "app/test.html",
     "test2.html": "app/test2.html",
     "js/myweb3.js": "web3-0.18.js",