title: "exclude" property of tsconfig.json is not being respected
body: <p>I am working with the excellent Express/Node/Typescript example code found <a href="https://github.com/czechboy0/Express-4x-Typescript-Sample" rel="noreferrer" title="here">here</a>. It transpiles the .ts code with the following command from run.sh:</p>
  
  <p><code>./node_modules/.bin/tsc --sourcemap --module commonjs ./bin/www.ts</code></p>
  
  <p>This works as advertised, but I would prefer to use a tsconfig.json file and <code>tsc -p .</code> However, when I run that command I get a raft of <code>TS2300: Duplicate identifier 'foo' errors</code>when <code>tsc</code>(erroneously?) tries to walk the <code>./node_modules</code> and <code>./typings</code> directories. Below is the tsconfig.json I am using:</p>
  
  <pre><code>{
    "compilerOptions": {
      "target": "ES5",
      "module": "commonjs",
      "moduleResolution": "node",
      "sourceMap": true,
      "emitDecoratorMetadata": true,
      "experimentalDecorators": true,
      "removeComments": false,
      "noImplicitAny": false
    },
    "exclude": [
      "node_modules",
      "typings"
    ]
  }
  </code></pre>
  
  <p>Any ideas? I am using tsc 1.7.3 FWIW.</p>