diff --git a/lib/pipeline.js b/lib/pipeline.js
index 8fa40d933..50c0dd526 100644
--- a/lib/pipeline.js
+++ b/lib/pipeline.js
@@ -16,13 +16,13 @@ Pipeline.prototype.build = function(abi) {
 
     // TODO: run the plugin here instead, for each file
 
-    var content = this.assetFiles[targetFile].map(file => {
+    var contentFiles = this.assetFiles[targetFile].map(file => {
       self.logger.info("reading " + file.filename);
 
       var pipelinePlugins = this.plugins.getPluginsFor('pipeline');
 
       if (file.filename === 'embark.js') {
-        return file.content + "\n" + abi;
+        return {content: file.content + "\n" + abi, filename: file.filename, path: file.path, modified: true};
       } else if (file.filename === 'embark-plugins.js') {
 
         var filesFromPlugins = [];
@@ -35,7 +35,7 @@ Pipeline.prototype.build = function(abi) {
               var fileObjects = plugin.runFilePipeline();
               for (var i=0; i < fileObjects.length; i++) {
                 var fileObject = fileObjects[i];
-                console.debug(JSON.stringify(fileObject));
+                //console.debug(JSON.stringify(fileObject));
                 filesFromPlugins.push(fileObject);
               }
             }
@@ -54,7 +54,7 @@ Pipeline.prototype.build = function(abi) {
                   console.log("skipping");
                   return;
                 }
-                file.content = plugin.runPipeline({targetFile: file.filename, source: file.content});
+                file.content = plugin.runPipeline({targetFile: file.filename, source: file.content, modified: true});
               }
               catch(err) {
                 self.logger.error(err.message);
@@ -64,16 +64,20 @@ Pipeline.prototype.build = function(abi) {
           return file.content;
         });
 
-        return fileContents.join('\n');
+        //return fileContents.join('\n');
+        return {content: fileContents.join('\n'), filename: "embark-plugins.js", path: "", modified: true};
 
       } else if (['web3.js', 'ipfs.js', 'ipfs-api.js', 'orbit.js'].indexOf(file.filename) >= 0) {
-        return file.content;
+        //return file.content;
+        file.modified = true;
+        return file;
       } else {
 
         if (pipelinePlugins.length > 0) {
           pipelinePlugins.forEach(function(plugin) {
             try {
               file.content = plugin.runPipeline({targetFile: file.filename, source: file.content});
+              file.modified = true;
             }
             catch(err) {
               self.logger.error(err.message);
@@ -81,16 +85,38 @@ Pipeline.prototype.build = function(abi) {
           });
         }
 
-        return file.content;
+        //return file.content;
+        return file;
       }
-    }).join("\n");
+    });
 
     var dir = targetFile.split('/').slice(0, -1).join('/');
     self.logger.info("creating dir " + this.buildDir + dir);
     mkdirp.sync(this.buildDir + dir);
 
-    self.logger.info("writing file " + this.buildDir + targetFile);
-    fs.writeFileSync(this.buildDir + targetFile, content);
+    // if it's a directory
+    if (targetFile.slice(-1) === '/' || targetFile.indexOf('.') === -1) {
+      var targetDir = targetFile;
+
+      if (targetDir.slice(-1) !== '/') {
+        targetDir = targetDir + '/';
+      }
+
+      contentFiles.map(function(file) {
+        var filename = file.filename.replace('app/', '');
+        filename = filename.replace(targetDir, '');
+        self.logger.info("writing file " + self.buildDir + targetDir + filename);
+
+        fs.writeFileSync(self.buildDir + targetDir + filename, fs.readFileSync(file.filename));
+      });
+    } else {
+      var content = contentFiles.map(function(file) {
+        return file.content;
+      }).join("\n");
+
+      self.logger.info("writing file " + this.buildDir + targetFile);
+      fs.writeFileSync(this.buildDir + targetFile, content);
+    }
   }
 };