[backport 1.2] Avoid downloading unused git submodules

Currently we have configuration in place to disable use of submodules, with the checkout-submodules git plugin option and the individual checkout options for each submodule, but these unused submodules are still downloaded at fetch time.

This patch fixes the plugin to just completely ignore the submodules which are configured to be unused.

This was previously fixed in the master branch by !996 (merged), and this patch backports the relevant fix to the 1.2 branch.

This fixes issue #804 (closed).