title: src/zone-flags.ts is missing from the TypeScript compilation after upgrading to Ionic 5
body: <p>I upgraded my Ionic 4 application by these two commands:</p>
  
  <pre class="lang-sh prettyprint-override"><code># Upgrading to Ionic 5
  npm install @ionic/angular@latest @ionic/angular-toolkit@latest --save
  
  # Upgrading to Angular 9
  ng update @angular/core @angular/cli
  </code></pre>
  
  <p>And when I did <code>ionic serve</code>, I started getting this error:</p>
  
  <pre><code>&gt; ng run app:serve --host=localhost --port=8100
  [ng] chunk {} 0.js, 0.js.map () 22.1 kB  [rendered]
  [ng] chunk {common} common.js, common.js.map (common) 25.7 kB  [rendered]
  [ng] 
  [ng] ERROR in ./src/zone-flags.ts
  [ng] Module build failed (from ./node_modules/@ngtools/webpack/src/index.js):
  [ng] Error: /Users/shashank/Projects/my-app/mobile-app/src/zone-flags.ts is missing from the TypeScript compilation. Please make sure it is in your tsconfig via the 'files' or 'include' property.
  [ng]     at AngularCompilerPlugin.getCompiledFile (/Users/shashank/Projects/my-app/mobile-app/node_modules/@ngtools/webpack/src/angular_compiler_plugin.js:909:23)
  [ng]     at plugin.done.then (/Users/shashank/Projects/my-app/mobile-app/node_modules/@ngtools/webpack/src/loader.js:41:31)
  [ng]     at process._tickCallback (internal/process/next_tick.js:68:7)
  </code></pre>