title: npm prune removes dependency module
body: <p>In my <code>package.json</code> file I have:</p>
  
  <pre><code>"dependencies": {
      "@aws/dynamodb-data-mapper": "^0.7.3",
      "@aws/dynamodb-data-mapper-annotations": "^0.7.3",
      "@my-company/common": "file:../common",
      ...
    }
  </code></pre>
  
  <p><code>@my-company/common</code> specifies a local module which is installed by yarn.</p>
  
  <p>However, when I run <code>npm prune</code>, this module is pruned.
  I thought that including it in the <code>package.json</code> <code>dependencies</code> object would stop it from being pruned? Did I miss something?</p>