title: VS2013 git - Project marked as pending delete
body: <p>I recently wanted to try VS2013 and the Git tool for SC. Everything worked great until I did something, but dont know what...
  I created a nodejs application and pushed it to github. However, the "main" script was not directly into the root repo directory, so I manually created another repo to be able to push it to heroku. Well,
  after that, another branch appeared in team explorer, and my master branch was told that all files were in a pending delete status. I sync the repo and it was well pushed into github however I must do it manually because I got an error in VS. Now that the repo is pushed, I dont have any error anymore when Sync, but there are still those pending delete status on every files.</p>
  
  <p>Furthermore, because of that, I cant do any change in a file and push it with VS, I must push manually.</p>
  
  <p>Any idea ? (I know the issue is really not clear, but I do my best ;))</p>