Issue title: Include doesn't import files from outDir
 Issue body: **TypeScript Version:**  2.0.0-beta

**Code**

tsconfig.json

``` json
{
  "compilerOptions": {
    "module": "commonjs",
    "target": "es5",
    "jsx": "react",
    "rootDir": "src",
    "outDir": "wwwroot",
    "typeRoots": [
      "node_modules/@types"
    ]
  },
  "include": [
    "src/**/*",
    "wwwroot/libs/**/*.d.ts"
  ]
}
```

**Expected behavior:**
All `.d.ts` files in `wwwroot/libs` folder should be imported in project.

**Actual behavior:** 
Files not imported and I get `Cannot find module` error.

When I change `outDir` to `wwwroot/app`, its work.

 Comments: 
 Comment 0: This should be working as intended in `thomasstephen@example.net`. 
 Comment 1: closing in favor of https://github.com/Microsoft/TypeScript/issues/12334
{'source': 'GithubIssues', 'repo_name_with_owner': 'microsoft/TypeScript', 'issue_id': 169546825, 'repo_stars': 85559.0}