upload_manifest.py: Allow an empty directory

Until now, our manifest did not support an empty directory, so we resorted
to uploading a file ".keep" inside the directory, which is kind of ugly
(this file remains in the final image).

Instead, in upload_manifest.py, if the given file is a directory (any
directory...), put it in the cpio as a directory, which causes an empty
directory to be created.

So now our images will no longer have files like /tmp/.keep.

Signed-off-by: Nadav Har'El <nyh@cloudius-systems.com>
Signed-off-by: Pekka Enberg <penberg@cloudius-systems.com>