diff --git a/lib/contracts/deploy.js b/lib/contracts/deploy.js
index d1b87ade..f37abec4 100644
--- a/lib/contracts/deploy.js
+++ b/lib/contracts/deploy.js
@@ -280,17 +280,17 @@ class Deploy {
 
           // calling each beforeDeploy handler declared by the plugin
           async.eachSeries(plugin.beforeDeploy, (beforeDeployFn, eachCb) => {
+            function beforeDeployCb(resObj){
+              contract.code = resObj.contractCode;
+              eachCb();
+            }
             beforeDeployFn({
               embarkDeploy:       self,
               pluginConfig:       plugin.pluginConfig,
               deploymentAccount:  deploymentAccount,
               contract:           contract,
-              callback:
-              (function(resObj){
-                contract.code = resObj.contractCode;
-                eachCb();
-              })
-            });
+              callback: beforeDeployCb
+            }, beforeDeployCb);
           }, () => {
             //self.logger.info('All beforeDeploy handlers of the plugin has processed.');
             eachPluginCb();
diff --git a/lib/core/config.js b/lib/core/config.js
index 89dd2b49..7061fadd 100644
--- a/lib/core/config.js
+++ b/lib/core/config.js
@@ -286,7 +286,7 @@ Config.prototype.loadFiles = function(files) {
     }
   });
   filesFromPlugins.filter(function(file) {
-    if (utils.fileMatchesPattern(files, file.intendedPath)) {
+    if ((file.intendedPath && utils.fileMatchesPattern(files, file.intendedPath)) || utils.fileMatchesPattern(files, file.file)) {
       readFiles.push(file);
     }
   });
diff --git a/test_apps/test_app/extensions/embark-service/fileInPipeline.js b/test_apps/test_app/extensions/embark-service/fileInPipeline.js
new file mode 100644
index 00000000..85f76853
--- /dev/null
+++ b/test_apps/test_app/extensions/embark-service/fileInPipeline.js
@@ -0,0 +1 @@
+console.log('File added to the pipeline using embark.addFileToPipeline');
diff --git a/test_apps/test_app/extensions/embark-service/index.js b/test_apps/test_app/extensions/embark-service/index.js
index 7b0d6261..be4f4366 100644
--- a/test_apps/test_app/extensions/embark-service/index.js
+++ b/test_apps/test_app/extensions/embark-service/index.js
@@ -19,4 +19,12 @@ module.exports = function (embark) {
     }
   });
   embark.addContractFile("./contracts/pluginSimpleStorage.sol");
+
+  embark.addFileToPipeline('./fileInPipeline.js');
+  embark.addFileToPipeline('./fileInPipeline.js', 'js/fileInPipeline.js');
+
+  embark.registerBeforeDeploy(function(options, callback) {
+    // Just calling register to prove it works. We don't actually want to change the contracts
+    callback({contractCode: options.contract.code});
+  });
 };
diff --git a/test_apps/test_app/package.json b/test_apps/test_app/package.json
index 8711dde1..80985c8d 100644
--- a/test_apps/test_app/package.json
+++ b/test_apps/test_app/package.json
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "bootstrap": "^3.3.6",
-    "embark-service": "./extensions/embark-service",
+    "embark-service": "file:extensions/embark-service",
     "jquery": "^1.11.3",
     "react": "^16.0.0",
     "react-bootstrap": "^0.32.0",