Could not load file or assembly Microsoft.Owin 3.0.0 to 3.0.1
<p>Interesting dependency issue...</p>

<p>VS2015.3, .NET45 updating Microsoft.Owin from 3.0.0 to 3.0.1 (traced this update to be the problem - wanting to install <a href="https://www.nuget.org/packages/IdentityServer3.AccessTokenValidation/" rel="noreferrer">https://www.nuget.org/packages/IdentityServer3.AccessTokenValidation/</a>)</p>

<p><a href="https://i.stack.imgur.com/cmBaA.png" rel="noreferrer"><img src="https://i.stack.imgur.com/cmBaA.png" alt="enter image description here"></a>
it works locally on IIS Express</p>

<p>but publish to Azure website: (am removing additional files at destination on azure publish straight from VS).  restarted and deleted all files from azure webserver too.</p>

<p><a href="https://i.stack.imgur.com/UNbNa.png" rel="noreferrer"><img src="https://i.stack.imgur.com/UNbNa.png" alt="enter image description here"></a></p>

<p>web.config translation looks okay</p>

<pre><code>&lt;dependentAssembly&gt;
   &lt;assemblyIdentity name="Microsoft.Owin" publicKeyToken="31bf3856ad364e35" culture="neutral" /&gt;
   &lt;bindingRedirect oldVersion="0.0.0.0-3.0.1.0" newVersion="3.0.1.0" /&gt;   
&lt;/dependentAssembly&gt;
</code></pre>

<p><strong>Edit</strong>
Bruce Chen's answer pointed me in the direction of Kudu (Azure - Development Tools, Advanced Tools)</p>

<p><a href="https://i.stack.imgur.com/Iq9By.png" rel="noreferrer"><img src="https://i.stack.imgur.com/Iq9By.png" alt="enter image description here"></a></p>

<p>I downloaded the Owin dll, and it was the wrong version ie 3.0.0</p>

<p>To fix I cleared out all package artifacts from my solution</p>

<p>git clean -xfd   (be careful)</p>

<p>Then rebuilt</p>