title: WebStorm "Warning:File was not compiled because there is no a reference from tsconfig.json"
body: <p>I am using WebStorm 2016.1.3 for an Angular 2 project with typescript. When I enable the ts compiler in WebStorm and modify a ts file (which should then be compiled) I get the following warning: <code>Warning:File was not compiled because there is no a reference from tsconfig.json</code> and the file is not compiled.</p>
  
  <p>My project file/folder structure is close to the style guide recommended by Angular 2:</p>
  
  <p>All my <code>ts</code> files are in a <code>script</code> folder. The root app is in that folder and every component has its own subfolder which contains one <code>ts</code> and one <code>html</code> file. Shared services etc are in a <code>Shared</code> subfolder.</p>
  
  <p>My <code>tsconfig</code> looks like this and is in the project root folder (the parent folder of the <code>script</code> folder):</p>
  
  <pre><code>{
    "compilerOptions": {
      "outDir": "wwwroot/app",
      "target": "es5",
      "module": "commonjs",
      "moduleResolution": "node",
      "inlineSourceMap": true,
      "inlineSources": true,
      "emitDecoratorMetadata": true,
      "experimentalDecorators": true,
      "removeComments": false,
      "noImplicitAny": false
    },
    "exclude": [
      "node_modules",
      "wwwroot"
    ]
  }
  </code></pre>
  
  <p>Except for the <code>ts</code> files directly in <code>script</code> all other in WebStorm opened and modified <code>ts</code> files result in the warning above and do not compile. In the typescript console in WebStorm the compiler says it was compiling the modified file (i.e. change detection seems to be working) but it does not emit a transpiled file. However, when WebStorm starts ALL <code>ts</code> files in all subfolders are correctly compiled. Also, if I use tsc manually or via gulp I get no issues and everything compiles as it should, which tells me that my <code>tsconfig</code> is OK.
  I tried specifying my own scope in WebStorm's typescript compiler options. Made no difference. The <code>Track changes</code> option is on. I tried it with and without the <code>Resolve objects using tsconfig.json</code> option on. Made no difference.</p>
  
  <p>I can't figure this thing out.
  Has anybody else encountered - and hopefully fixed - this issue?</p>