title: Typescript build with project references fails with `Output file has not been built from source file` even though it was built
body: <p>I'm trying to build a project that references a shared project alongside it. 
  My configs look like:</p>
  
  <p><code>projectA/tsconfig.json</code>:</p>
  
  <pre><code>{
    "compilerOptions": {
      "module": "commonjs",
      "noImplicitReturns": true,
      "lib": [
        "esnext.asynciterable"
      ],
      "noUnusedLocals": true,
      "outDir": "lib",
      "sourceMap": true,
      "strict": true,
      "target": "es2017"
    },
    "compileOnSave": true,
    "include": [
      "src"
    ],
    "references": [
      {
        "path": "../shared",
        "prepend": true
      }
    ]
  }
  </code></pre>
  
  <p><code>shared/tsconfig.json</code>:</p>
  
  <pre><code>{
    "compilerOptions": {
      "outFile": "build/out.js",
      "composite": true,
      "target": "es5",
      "module": "amd",
      "declaration": true,
      "strict": true,
      "moduleResolution": "node",
      "esModuleInterop": true,
      "forceConsistentCasingInFileNames": true
    },
    "include": [
      "src"
    ]
  }
  </code></pre>
  
  <p>running <code>ts -b</code> from inside <code>projectA</code> yields:</p>
  
  <pre><code>src/index.ts:6:24 - error TS6305: Output file '.../shared/build/out.d.ts' has not been built from source file '.../shared/src/index.ts'.
  
  6 import DummyClass from '../../shared/src';
  </code></pre>
  
  <p><strong>Even though this file is indeed created.</strong></p>
  
  <p>What am I doing wrong?</p>