upload-pack: send refs' objects despite "filter"

A filter line in a request to upload-pack filters out objects regardless
of whether they are directly referenced by a "want" line or not. This
means that cloning with "--filter=blob:none" (or another filter that
excludes blobs) from a repository with at least one ref pointing to a
blob (for example, the Git repository itself) results in output like the
following:

    error: missing object referenced by 'refs/tags/junio-gpg-pub'

and if that particular blob is not referenced by a fetched tree, the
resulting clone fails fsck because there is no object from the remote to
vouch that the missing object is a promisor object.

Update both the protocol and the upload-pack implementation to include
all explicitly specified "want" objects in the packfile regardless of
the filter specification.

Signed-off-by: Jonathan Tan <jonathantanmy@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

revision.c

@@ -172,6 +172,7 @@ static void add_pending_object_with_path(struct rev_info *revs,
 		strbuf_release(&buf);
 		return; /* do not add the commit itself */
 	}
+	obj->flags |= USER_GIVEN;
 	add_object_array_with_path(obj, name, &revs->pending, mode, path);
 }