diff --git a/lib/build/bundle.js b/lib/build/bundle.js
index 62eec2a52..3bcf2ff49 100644
--- a/lib/build/bundle.js
+++ b/lib/build/bundle.js
@@ -268,21 +268,16 @@ exports.Bundle = class {
       for (let i = 0; i < files.length; ++i) {
         let currentFile = files[i];
         let sourceMapEnabled = buildOptions.isApplicable('sourcemaps');
-        let sourceMap = sourceMapEnabled ? currentFile.sourceMap : undefined;
-
-        function fileIsDependency(file) {
-          return file
-            && file.path
-            && file.path.indexOf('node_modules') >= 0;
-        }
+        let sourceMap = sourceMapEnabled && currentFile.sourceMap ?
+          JSON.parse(JSON.stringify(currentFile.sourceMap)) :
+          undefined;
+        let parsedPath = currentFile.path && path.parse(currentFile.path);
 
         function acquireSourceMapForDependency(file) {
           if (!file || !file.path) {
             return;
           }
 
-          let parsedPath = path.parse(file.path);
-
           try {
             let base64SourceMap = Convert.fromSource(file.contents.toString());
 
@@ -307,30 +302,39 @@ exports.Bundle = class {
             ? converter.sourcemap
             : null;
 
-          if (sourceMap !== null) {
-            let sourceRoot = parsedPath.dir.slice(process.cwd().length);
-            sourceMap.sourceRoot = sourceRoot.replace(/\\/g, '\/');
-          }
-
           return sourceMap;
         }
 
         let content = currentFile.contents;
 
         if (sourceMapEnabled) {
-          if (fileIsDependency(currentFile)) {
+          if (!sourceMap) {
             sourceMap = acquireSourceMapForDependency(currentFile);
           }
 
-          if (sourceMap) {
+          if (sourceMap && parsedPath) {
+            let sourceRoot = parsedPath.dir.slice(process.cwd().length + 1);
+            sourceMap.sourceRoot = sourceRoot.replace(/\\/g, '\/');
             needsSourceMap = true;
             content = Convert.removeMapFileComments(currentFile.contents);
           }
+
+          if (sourceMap && !sourceMap.mappings) {
+            // Need a dummy identity map.
+            // Otherwise concat-with-sourcemaps is confused about source path.
+            sourceMap.mappings = 'AAAA';
+          }
         }
-        concat.add(currentFile.path, content, sourceMap ? JSON.stringify(sourceMap) : undefined);
+
+
+        concat.add(
+          currentFile.path ? path.relative(process.cwd(), currentFile.path) : null,
+          content,
+          sourceMap ? JSON.stringify(sourceMap) : undefined
+        );
       }
 
-      let mapContents;
+      let bundleMap;
       let contents = concat.content;
       let bundleFileName = this.config.name;
 
@@ -414,11 +418,11 @@ exports.Bundle = class {
         if (minificationResult.error) throw minificationResult.error;
 
         contents = minificationResult.code;
-        mapContents = needsSourceMap ? Convert.fromJSON(minificationResult.map).toJSON() : undefined;
+        bundleMap = needsSourceMap ? Convert.fromJSON(minificationResult.map).toObject() : undefined;
       } else if (needsSourceMap) {
-        mapContents = Convert.fromJSON(concat.sourceMap)
+        bundleMap = Convert.fromJSON(concat.sourceMap)
           .setProperty('sourceRoot', mapSourceRoot)
-          .toJSON();
+          .toObject();
 
         contents += os.EOL + '//# sourceMappingURL=' +  path.basename(mapFileName);
       }
@@ -426,8 +430,14 @@ exports.Bundle = class {
       return fs.writeFile(path.posix.join(platform.output, bundleFileName), contents).then(() => {
         this.requiresBuild = false;
 
-        if (mapContents) {
-          return fs.writeFile(path.posix.join(platform.output, mapFileName), mapContents)
+        if (bundleMap) {
+          const sourceRoot = bundleMap.sourceRoot;
+          if (sourceRoot) {
+            // Remove sourceRoot in order to be nicer to karma code coverage tool.
+            delete bundleMap.sourceRoot;
+            bundleMap.sources = bundleMap.sources.map(s => path.posix.join(sourceRoot, s));
+          }
+          return fs.writeFile(path.posix.join(platform.output, mapFileName), JSON.stringify(bundleMap))
             .catch(e => {
               logger.error(`Unable to write the sourcemap to ${path.posix.join(platform.output, mapFileName)}`);
             });