When "sym" is a symbolic link that is inside the working tree, and it
points at a directory "dir" that has "path" in it, "update-index --add
sym/path" used to mistakenly add "sym/path" as if "sym" were a normal
directory.

"git apply", "git diff" and "git merge" have been taught about this issue
some time ago, but "update-index" and "add" have been left ignorant for
too long.

Signed-off-by: Junio C Hamano <gitster@pobox.com>