Fix clone --branches
    
    When cloning with the --branches option we first clone a bare repo
    locally, then clone each branch from that bare repo.  Avoid adding an
    excludes file to the temporary bare repo (which fails because we pass
    the wrong path to the git dir).  Add an excludes file to each branch
    dir.
    
    Resolves: rhbz#1707223
    Signed-off-by: Todd Zullinger <tmz@pobox.com>