title: How to fix org.eclipse.jgit.api.errors.JGitInternalException:Entry not found by path Exception while doing commit using Egit
body: <p>I am trying to integrate Git in my existing RCP application,
  For that i have imported egit.core and egit.io plugin as source project into my application and when i tried to commit the file using egit's commit() from CommitOperation Class i am getting the below exception:</p>
  
  <pre><code>Caused by: org.eclipse.jgit.api.errors.JGitInternalException: Entry not found by path: D:\Test\file.txt
  at org.eclipse.jgit.api.CommitCommand.createTemporaryIndex(CommitCommand.java:414)
  at org.eclipse.jgit.api.CommitCommand.call(CommitCommand.java:194)
  at org.eclipse.egit.core.op.CommitOperation.commit(CommitOperation.java:255)
  ... 39 more
  </code></pre>
  
  <p>And when i debugged through the code to find out where the  exception is happening, it is on CommitCommand.class at the following point</p>
  
  <pre><code>// there must be no unprocessed paths left at this point; otherwise an
      // untracked or unknown path has been specified
      for (int i = 0; i &lt; onlyProcessed.length; i++)
          if (!onlyProcessed[i])
              throw new JGitInternalException(MessageFormat.format(
                      JGitText.get().entryNotFoundByPath, only.get(i)));
  </code></pre>
  
  <p>I have no idea what the unprocessed path here is meant by? 
  I am able to access the path. can anyone help me how to proceed further</p>