title: MissingObjectException while update submodules with JGit
body: <p>I am trying to update submodules:</p>
  
  <pre class="lang-java prettyprint-override"><code>git.submoduleUpdate().call()
  </code></pre>
  
  <p>but I get:</p>
  
  <pre><code>org.eclipse.jgit.api.errors.JGitInternalException: Missing unknown e88da827bdc5c5a4b0d87b8be79b81567759411b
      at org.eclipse.jgit.api.SubmoduleUpdateCommand.call(SubmoduleUpdateCommand.java:211)
      at kontinuum.WorkPackageProcessorKt.processWorkPackages(WorkPackageProcessor.kt:43)
      at kontinuum.MainKt.main(Main.kt:30)
  Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing unknown e88da827bdc5c5a4b0d87b8be79b81567759411b
      at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:145)
      at org.eclipse.jgit.lib.ObjectReader.open(ObjectReader.java:226)
      at org.eclipse.jgit.revwalk.RevWalk.parseAny(RevWalk.java:859)
      at org.eclipse.jgit.revwalk.RevWalk.parseCommit(RevWalk.java:772)
      at org.eclipse.jgit.api.SubmoduleUpdateCommand.call(SubmoduleUpdateCommand.java:175)
      ... 2 more
  </code></pre>
  
  <p>Interestingly on the console it works:</p>
  
  <pre><code>kontinuum@ligi-tp ~/k/w/l/SurvivalManual&gt; git submodule update
  remote: Counting objects: 27, done.
  remote: Compressing objects: 100% (27/27), done.
  remote: Total 27 (delta 17), reused 0 (delta 0), pack-reused 0
  Unpacking objects: 100% (27/27), done.
  From https://github.com/ligi/SurvivalManual.wiki
     b72e23e..e88da82  master     -&gt; origin/master
  Submodule path 'android/src/main/assets/md': checked out 'e88da827bdc5c5a4b0d87b8be79b81567759411b'
  </code></pre>