submodules: Support for --reference when cloning submodules

This update extends project cache directory support to submodules. All
submodules can be updated in the project cache by running the following
command from the top-level cache directory:

git submodule update --init --checkout --recursive --force
or by cloning with git clone --recurse-submodules

Signed-off-by: Jean-Philippe Brucker <jean-philippe@linaro.org>
Signed-off-by: Aneesh Kumar K.V (Arm) <aneesh.kumar@kernel.org>