now accepts config file

test/assets/customcompiled.d.ts

@@ -0,0 +1 @@
+declare var hello: string;

test/assets/customcompiled.js

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+
+var hello = "hello";

test/assets/customdir/custom.js

@@ -0,0 +1,2 @@
+var hello = "hello";
+//# sourceMappingURL=custom.js.map

test/assets/customdir/custom.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"custom.js","sourceRoot":"","sources":["custom.ts"],"names":[],"mappings":"AAAA,IAAI,KAAK,GAAG,OAAO,CAAC"}

test/assets/customdir/custom.ts

@@ -0,0 +1 @@
+var hello = "hello";

test/assets/customdir/typings.json

@@ -0,0 +1,7 @@
+{
+  "ambientDependencies": {
+    "node": "github:DefinitelyTyped/DefinitelyTyped/node/node.d.ts#78d36dd49b6b55b9fdfe61776a12bf05c8b07777",
+    "colors": "github:DefinitelyTyped/DefinitelyTyped/colors/colors.d.ts#09e37435ffb2c56a6f908081194a74756f24f99d",
+    "vinyl": "github:DefinitelyTyped/DefinitelyTyped/vinyl/vinyl.d.ts#78d36dd49b6b55b9fdfe61776a12bf05c8b07777"
+  }
+}

test/assets/npmts.json

@@ -0,0 +1,9 @@
+{
+  "mode":"custom",
+  "ts":{
+    "./customdir/custom.ts":"./customcompiled.js"
+  },
+  "typings":[
+    "./customdir"
+  ]
+}