title: Bazel build not respecting my git submodules
body: <p>I'm running a <code>bazel build</code> in a project that is composed of git submodules, 
  with the following structure:</p>
  
  <pre><code>/work/
  ├── tensorflow/ [git submodule]
  └── train/
      └── DeepSpeech/ [git submodule]
          └── native_client/
  </code></pre>
  
  <p>The build command looks like this:</p>
  
  <pre><code>bazel build \
      --config=monolithic \
      -c opt \
      --copt=-O3 \
      --copt="-D_GLIBCXX_USE_CXX11_ABI=0" \
      --copt=-fvisibility=hidden \
      //native_client:libdeepspeech.so \
      //native_client:generate_trie
  </code></pre>
  
  <p>and I'm getting the following error: </p>
  
  <pre><code>ERROR: /work/tensorflow/native_client/BUILD:6:1: Executing genrule //native_client:ds_git_version failed (Exit 1)
  realpath: /work/train/DeepSpeech/native_client/../.git/: Not a directory
  </code></pre>
  
  <p>It seems to be complaining that <code>/work/train/DeepSpeech/.git</code> isn't a directory, and it would be correct because <code>/work/train/DeepSpeech/.git</code> is a file, containing the path to the the git tree of the git submodule.</p>
  
  <p>Here are the contents of <code>/work/train/DeepSpeech/.git</code>:</p>
  
  <pre><code>gitdir: ../../.git/modules/train/DeepSpeech
  </code></pre>
  
  <p>My question is: Is there a way to have bazel respect the submodule structure of my repository? Ideally, there would be some flags I could pass in my <code>bazel build</code> command that would make it magically work, but I'm open to other options.</p>
  
  <p>Thanks for your help!</p>