Fix more from testing:
1) Move all sync-related tasks to "doSync" so we can rearrange
   certain operations easily - specifically delaying the get
   of GitRepo.
2) Fix that a commit is done when loading an existing JGit Repo.
   This breaks the assertion that a commit is done while in a
   merge conflict state. (Occurs when restarting and accessing
   an existing local repo for the first time that has merge conflicts
   from previous session.)