[PATCHv2 6/6] clone: reference flag is used for submodules as well

When giving a --reference while also giving --recurse, the alternates for the submodules are assumed to be in the superproject as well. In case they are not, we error out when cloning the submodule. However we error out completely, we did not record the alternates yet, so a following update

[PATCHv2 6/6] clone: reference flag is used for submodules as well

When giving a --reference while also giving --recurse, the alternates for the submodules are assumed to be in the superproject as well. In case they are not, we error out when cloning the submodule. However we error out completely, we did not record the alternates yet, so a following update