filter-branch: Fix to allow replacing submodules with another content

filter-branch: Fix to allow replacing submodules with another content

When git filter-branch is used to replace a submodule with another
content, it always fails on the first commit.

Consider a repository with submod directory containing a submodule.  The
following command to remove the submodule and replace it with a file fails:

    git filter-branch --tree-filter 'rm -rf submod &&
                                     git rm -q submod &&
                                     mkdir submod &&
                                     touch submod/file'

with an error:

    error: submod: is a directory - add files inside instead

The reason is that git diff-index, which generates the first part of the
list of files updated by the tree filter, emits also the removed submodule
even if it was replaced by a real directory.

Signed-off-by: Michal Sojka <sojkam1@fel.cvut.cz>
Signed-off-by: Junio C Hamano <gitster@pobox.com>