diff --git a/lib/core/config.js b/lib/core/config.js
index a28d41272..be23c6744 100644
--- a/lib/core/config.js
+++ b/lib/core/config.js
@@ -2,6 +2,7 @@ var fs = require('./fs.js');
 var File = require('./file.js');
 var Plugins = require('./plugins.js');
 var utils = require('../utils/utils.js');
+var path = require('path');
 
 var Config = function(options) {
   this.env = options.env;
@@ -188,6 +189,18 @@ Config.prototype.loadChainTrackerFile = function() {
   this.chainTracker = fs.readJSONSync(this.chainsFile);
 };
 
+function findMatchingExpression(filename, filesExpressions) {
+  for (let fileExpression of filesExpressions) {
+    var matchingFiles = utils.filesMatchingPattern(fileExpression);
+    for (matchFile of matchingFiles) {
+      if (matchFile === filename) {
+        return path.dirname(fileExpression).replace(/\*/g, '')
+      }
+    }
+  }
+  return path.dirname(filename)
+}
+
 Config.prototype.loadFiles = function(files) {
   var self = this;
   var originalFiles = utils.filesMatchingPattern(files);
@@ -196,7 +209,8 @@ Config.prototype.loadFiles = function(files) {
   originalFiles.filter(function(file) {
     return (file[0] === '$' || file.indexOf('.') >= 0);
   }).filter(function(file) {
-    readFiles.push(new File({filename: file, type: "dapp_file", path: file}));
+    let basedir = findMatchingExpression(file, files);
+    readFiles.push(new File({filename: file, type: "dapp_file", basedir: basedir, path: file}));
   });
 
   var filesFromPlugins = [];
diff --git a/lib/core/file.js b/lib/core/file.js
index adce6ab0c..98e49c0c5 100644
--- a/lib/core/file.js
+++ b/lib/core/file.js
@@ -6,6 +6,7 @@ class File {
     this.filename = options.filename;
     this.type = options.type;
     this.path = options.path;
+    this.basedir = options.basedir;
     this.resolver = options.resolver;
   }
 
diff --git a/lib/pipeline/pipeline.js b/lib/pipeline/pipeline.js
index d0eb8aef9..de1a9565e 100644
--- a/lib/pipeline/pipeline.js
+++ b/lib/pipeline/pipeline.js
@@ -111,12 +111,12 @@ class Pipeline {
                   return fileCb("couldn't find file: " + file.filename);
                 }
                 let fileContent = fs.readFileSync('./.embark/' + file.filename).toString();
-                fileCb(null, {content: fileContent, filename: file.filename, path: file.path, modified: true});
+                fileCb(null, {content: fileContent, filename: file.filename, path: file.path, basedir: file.basedir, modified: true});
               });
 
           } else {
             file.content(function(fileContent) {
-              return fileCb(null, {content: fileContent, filename: file.filename, path: file.path, modified: true});
+              return fileCb(null, {content: fileContent, filename: file.filename, path: file.path, basedir: file.basedir, modified: true});
             });
           }
 
@@ -138,8 +138,7 @@ class Pipeline {
             }
 
             contentFiles.map(function (file) {
-              let filename = file.filename.replace('app/', '');
-              filename = filename.replace(targetDir, '');
+              let filename = file.filename.replace(file.basedir + '/', '');
               self.logger.info("writing file " + (self.buildDir + targetDir + filename).bold.dim);
 
               fs.copySync(file.path, self.buildDir + targetDir + filename, {overwrite: true});