Fix tests for removing defaults
    
    The tests were not accounting for the removal of a file. This
    patch changes the get_index_and_defaults() function to return
    FileNotFoundError instead of IOError when the file does not
    exist for a commit and then changes the logic of the consuming
    function to handle IOError and FileNotFoundError appropriately.
    
    Signed-off-by: Stephen Gallagher <sgallagh@redhat.com>