Fix _ReferenceGitDir symlinking

This fixes these errors:

  ...
  File ".repo/repo/project.py", line 2371, in _ReferenceGitDir
    os.symlink(os.path.relpath(src, os.path.dirname(dst)), dst)
  OSError: [Errno 17] File exists

Which was happening for checkouts that were created before v1.12.8, when
project-objects was created. Nothing had yet been forcing these
checkouts to use project-objects, until the recent verification changes.

In this OSError case, we already created the symlink, so src == dst, and
the directory did not exist. This caused us to run os.makedirs the
os.symlink on the same file.

dst really should be the file in gitdir, not the target of that symlink
if it exists. So just use realpath for the dotgit portion of the path.

Change-Id: Iff5396a2093de91029c42cf38aa57131fd22981c