apply: check D/F conflicts more carefully.

When creating a new file where a directory used to be (or the user had
an empty directory) the code did not check the result from lstat() closely
enough, and mistakenly thought the path already existed in the working tree.

This does not fix the problem where you have a patch that creates a file
at "foo" and removes a file at "foo/bar" (which presumably is the last file
in "foo/" directory in the original).  For that, we would need to restructure
write_out_results() loop.

Signed-off-by: Junio C Hamano <junkio@cox.net>

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