title: Files missing after git merge
body: <p>I have read other questions in regards to this, but mine is a peculiar case of losing files in local git, without a trace.</p>
  
  <p>I cloned a repository:</p>
  
  <pre><code> git clone https://github.com/uruddarraju/kubernetes
   cd kubernetes/
  </code></pre>
  
  <p>I did a fetch of upstream for project kubernetes using the following commands:</p>
  
  <pre><code> git remote add upstrm https://github.com/kubernetes/kubernetes
   git fetch upstrm
  </code></pre>
  
  <p>This brought down a bunch of tags as follows:</p>
  
  <pre><code>uruddarraju$ git tag
  v1.3.2-beta.0
  v1.3.3
  v1.3.3-beta.0
  v1.3.4
  </code></pre>
  
  <p>I am trying to merge v1.3.4 into the branch tess or remote origin</p>
  
  <pre><code>git merge v1.3.4
  </code></pre>
  
  <p>There are a lot of merge conflicts which I have  to resolve, but interestingly I also see that a new file that is added to upstrm/v1.3.4 is now missing in the local file system and I don't see that file in git status either.</p>
  
  <p>How can this be possible ? I was expecting these files to be added as part of the merge but clearly they were not. </p>
  
  <pre><code>uruddarraju$ ls pkg/genericapiserver/
  resource_encoding_config.go
  </code></pre>
  
  <p>I am looking for the file resource_config.go
  I discarded the merge and checked into v1.3.4 to verify if the file is present in that branch:</p>
  
  <pre><code>uruddarraju$ git checkout -b merege1.3 v1.3.4
  uruddarraju$ ls pkg/genericapiserver
  resource_config.go
  resource_config_test.go
  resource_encoding_config.go
  </code></pre>
  
  <p>I did a git diff on the two branches and I clearly see that the files have been added in upstrm/v1.3.4
  I ran the following while I was on v1.3.4</p>
  
  <pre><code>uruddarraju$ git diff master --name-status
  A       pkg/genericapiserver/resource_config.go
  A       pkg/genericapiserver/resource_config_test.go
  A       pkg/genericapiserver/resource_encoding_config.go
  </code></pre>
  
  <p>When I do the other way around, bu being on master and doing a diff with v1.3.4, I see:</p>
  
  <pre><code>uruddarraju$ git diff v1.3.4 --name-status
  D       pkg/genericapiserver/resource_config.go
  D       pkg/genericapiserver/resource_config_test.go
  D       pkg/genericapiserver/resource_encoding_config.go
  </code></pre>
  
  <p><strong>EDIT 1:</strong></p>
  
  <p>The merge base is as shown below:</p>
  
  <pre><code>uruddarraju$ git merge-base --all HEAD v1.3.4
  812b9a47d6625b0fd02af18f9b147720f3c6bfce
  </code></pre>
  
  <p><strong>EDIT 2:</strong></p>
  
  <p>I also see the following warning:</p>
  
  <pre><code>warning: inexact rename detection was skipped due to too many files.
  warning: you may want to set your merge.renamelimit variable to at least 4292 and retry the command.
  </code></pre>
  
  <p>I am clearly missing something. Any help would be appreciated.</p>