title: switching between branches where a subdirectory was in the main repo vs. submodularized
body: <p>We've made a subdirectory S into a separate repo and re-added it as a submodule in a branch B.  Now when I want to switch back to the original branch A, where the subdirectory was checked into the original repo, git complains that the stuff from the submodule is untracked and has to be moved away first.  Can we switch back to A at all without manually dragging the S away and they moving it back in for B?</p>
  
  <p>Update: the comments below indicate it may be a deficiency of the old branch and git not willing to do a smart thing here.  Is this so, and what kind of rebasing, if any, of the original branch with S in the main repo can let it coexist and be checkout-able at any time vs. the submodularized version?</p>