Context :

• gulp-typesrcipt : 3.1.3 (last version)
• typescript : 2.0.10
• Visual Studio 2015
• Windows 7 64 bits

I have an unwanted sub directory in my destination folder.
Here is the structure of my project, with source and output :

Important points are :

• my gulp file is at the root of the project
• I have a ts directory containing my tsconfig file and a sub directory app containing ts files
• the build output is the wwwroot/js directory

So my gulp file and tsconfig file are not in the same directory (I can not move the tsconfig file at the project root, else intellisense does not work in visual studio)

I want that the compiled app.js file be created in the wwwroot/js directory not in the wwwroot/js/ts directory.

Here is my gulpfile

var tsProject = ts.createProject('ts/tsconfig.json', { rootDir: "app", outFile: 'app.js' });
gulp.task("ts", function () {
  return tsProject
     .src()
     .pipe(tsProject())
     .js
     .pipe(gulp.dest("./wwwroot/js/"));
});

My tsconfig

{
  "compilerOptions": {
    "target": "es5",
    "module": "system",
    "moduleResolution": "node",
    "experimentalDecorators": true,
    "noImplicitAny": false,
    "noEmitOnError": true,
    "sourceMap": true,
    "removeComments": false,
    "emitDecoratorMetadata": true
  },
  "exclude": [
    "../node_modules",
    "../wwwroot"
  ]
}