diff --git a/index.js b/index.js
index 66aab5c..2931289 100644
--- a/index.js
+++ b/index.js
@@ -5,7 +5,7 @@ function cssDependencies( data, which ) {
 		regexp = new RegExp( "\\/\\/>>\\s*css\\." + which + ":(.*)", "g" );
 
 	data.replace( regexp, function( garbage, input ) {
-		input = input.split( "," ).map( trim ); 
+		input = input.split( "," ).map( trim );
 		result.push.apply( result, input );
 	});
 
@@ -15,15 +15,11 @@ function cssDependencies( data, which ) {
 }
 
 function jsDependencies( data ) {
-	var match,
-		result = [];
-
-	match = data.match( /define\(\[([^\]]*?)\]/ );
-	if ( match !== null ) {
-		result = match[ 1 ].split( "," ).map( trim );
+	var match = data.match( /define\(\[([^\]]*?)\]/ );
+	if ( match === null ) {
+		return [];
 	}
-	
-	return result;
+	return match[ 1 ].replace( /\/\/.+/g, "" ).split( "," ).map( trim );
 }
 
 /**
diff --git a/test/fixtures/basic/foo.js b/test/fixtures/basic/foo.js
index 52736fc..7052c3c 100644
--- a/test/fixtures/basic/foo.js
+++ b/test/fixtures/basic/foo.js
@@ -1,2 +1,6 @@
 //>> css.baz: ./foo.css
-define([ "./bar" ]);
+define([
+
+	// comment
+	"./bar"
+]);
diff --git a/test/fixtures/nested/theme/input.css b/test/fixtures/nested/theme/input.css
new file mode 100644
index 0000000..c4236fe
--- /dev/null
+++ b/test/fixtures/nested/theme/input.css
@@ -0,0 +1 @@
+input {}
diff --git a/test/fixtures/nested/theme/version.css b/test/fixtures/nested/theme/version.css
new file mode 100644
index 0000000..208d16d
--- /dev/null
+++ b/test/fixtures/nested/theme/version.css
@@ -0,0 +1 @@
+body {}
diff --git a/test/fixtures/nested/version.js b/test/fixtures/nested/version.js
new file mode 100644
index 0000000..1ad525d
--- /dev/null
+++ b/test/fixtures/nested/version.js
@@ -0,0 +1,2 @@
+//>> css.structure: ./theme/version.css
+define("0.2.0");
diff --git a/test/fixtures/nested/widgets/input.js b/test/fixtures/nested/widgets/input.js
new file mode 100644
index 0000000..adcbdaa
--- /dev/null
+++ b/test/fixtures/nested/widgets/input.js
@@ -0,0 +1,3 @@
+//>> css.structure: ../theme/input.css
+define(["../version"], function(version) {
+});
diff --git a/test/index.js b/test/index.js
index bf1e0d0..82bed37 100644
--- a/test/index.js
+++ b/test/index.js
@@ -49,6 +49,28 @@ describe( "jQuery CSS Builder", function() {
 
 	});
 
+	describe( "Basic - nested+appdir", function() {
+		var css,
+			files = {
+				"fixtures/version.js": fs.readFileSync( __dirname + "/fixtures/nested/version.js" ),
+				"fixtures/widgets/input.js": fs.readFileSync( __dirname + "/fixtures/nested/widgets/input.js" ),
+				"fixtures/theme/version.css": fs.readFileSync( __dirname + "/fixtures/nested/theme/version.css" ),
+				"fixtures/theme/input.css": fs.readFileSync( __dirname + "/fixtures/nested/theme/input.css" )
+			};
+
+		before(function( done ) {
+			jQueryCSSBuilder( files, "structure", { appDir: "fixtures", include: [ "widgets/input" ] }, function( error, _css ) {
+				css = _css;
+				done( error );
+			});
+		});
+
+		it( "should build just fine", function() {
+			expect( css ).to.equal( "input {}\nbody {}\n" );
+		});
+
+	});
+
 	describe( "Two bundles", function() {
 		var cssNorth, cssSouth;
 		var files = {