<p dir="auto"><strong>Summary</strong></p>
<p dir="auto">Apologies if this is not the right place to log this, but I seem to have the exact same issue as described here:</p>
<p dir="auto"><a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="119993977" data-permission-text="Title is private" data-url="https://github.com/microsoft/TypeScript/issues/5894" data-hovercard-type="issue" data-hovercard-url="/microsoft/TypeScript/issues/5894/hovercard" href="https://github.com/microsoft/TypeScript/issues/5894">#5894</a></p>
<p dir="auto">but with VS2015 and the latest release of Typescript tools (1.8.6)</p>
<p dir="auto">I've attached a sample project illustrating the issue. Essentially it's an empty web application with a single app.ts typescript file in a src folder, and a tsconfig.json file redirecting the output to a folder wwwroot.</p>
<p dir="auto"><strong>TypeScript Version:</strong><br>
1.7.5 (according to tsc -v from commandline - not really sure if Visual studio uses the same?)<br>
Typescript tools for Visual Studio: 1.8.6.0</p>
<p dir="auto"><strong>Code</strong></p>
<div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="{
  &quot;compilerOptions&quot;: {
    &quot;noImplicitAny&quot;: false,
    &quot;noEmitOnError&quot;: true,
    &quot;removeComments&quot;: false,
    &quot;sourceMap&quot;: true,
    &quot;target&quot;: &quot;es5&quot;,
    &quot;outDir&quot;: &quot;./wwwroot/&quot;
  },
  &quot;exclude&quot;: [
    &quot;node_modules&quot;,
    &quot;wwwroot&quot;
  ]
}"><pre class="notranslate"><code class="notranslate">{
  "compilerOptions": {
    "noImplicitAny": false,
    "noEmitOnError": true,
    "removeComments": false,
    "sourceMap": true,
    "target": "es5",
    "outDir": "./wwwroot/"
  },
  "exclude": [
    "node_modules",
    "wwwroot"
  ]
}
</code></pre></div>
<p dir="auto"><a href="https://github.com/Microsoft/TypeScript/files/196950/TSTest.zip">TSTest.zip</a></p>
<p dir="auto"><strong>Expected behavior:</strong></p>
<p dir="auto">I can publish the project using File System publish method</p>
<p dir="auto"><strong>Actual behavior:</strong></p>
<p dir="auto">The publish fails with the error message:</p>
<p dir="auto">Copying file src\app.js to obj\Release\Package\PackageTmp\src\app.js failed. Could not find file 'src\app.js'.</p>
<p dir="auto">Hi, I have a problem publishing an asp.net 4 app using angular, ts 1.8 from visual studio.<br>
Since with ts 1.8 is possible to add a tsconfig file in asp.net 4 projects too, I added it and configured it to create a single output file this way</p>
<div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="{
  &quot;compilerOptions&quot;: {
    &quot;noImplicitAny&quot;: false,
    &quot;noEmitOnError&quot;: true,
    &quot;removeComments&quot;: false,
    &quot;target&quot;: &quot;es5&quot;,
    &quot;inlineSourceMap&quot;: true,
    &quot;inlineSources&quot;: true,
    &quot;outFile&quot;: &quot;Scripts/application.js&quot;
  },
  &quot;exclude&quot;: [
    &quot;node_modules&quot;,
    &quot;wwwroot&quot;
  ]
}
"><pre class="notranslate"><code class="notranslate">{
  "compilerOptions": {
    "noImplicitAny": false,
    "noEmitOnError": true,
    "removeComments": false,
    "target": "es5",
    "inlineSourceMap": true,
    "inlineSources": true,
    "outFile": "Scripts/application.js"
  },
  "exclude": [
    "node_modules",
    "wwwroot"
  ]
}

</code></pre></div>
<p dir="auto">All works fine until I try to deploy to an azure app service using web deploy: added it, configured, but when I try to deploy I have this error:</p>
<p dir="auto"><code class="notranslate">Copying file App\Maintenance.js to obj\Debug\Package\PackageTmp\App\Maintenance.js failed. Could not find file 'App\Maintenance.js'.  </code></p>
<p dir="auto">This is one the ts files that are compiled in the single file 'application.js'.<br>
If my ts installation is not broken, looks like web deploy still continues to look inside the msbuild project settings for the deployment settings of ts files, but adding tsconfig.json file this changes, and when tsconfig file is present typescript project settings are disabled.</p>
<p dir="auto">Proof of this is that if I rename the tsconfig file, reapply settings via project settings and try to deploy, everything works fine.</p>
<p dir="auto">Is this normal?</p>