Commit d89c1dfa (filter-branch: don't use xargs -0, 2008-03-12) replaced a
'ls-files | xargs rm' pipeline by 'git clean'. 'git clean' however does
not recurse and remove directories by default.

Now, consider a tree-filter that renames a directory.

  1. For the first commit everything works as expected

  2. Then filter-branch checks out the files for the next commit. This
     leaves the new directory behind because there is no real "branch
     switching" involved that would notice that the directory can be
     removed.

  3. Then filter-branch invokes 'git clean' to remove exactly those
     left-overs. But here it does not remove the directory.

  4. The next tree-filter does not work as expected because there already
     exists a directory with the new name.

Just add -d to 'git clean', so that empty directories are removed.
Signed-off-by: NJohannes Sixt <johannes.sixt@telecom.at>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>