Ensure submodules are checked out on the deployment server

If checkout_submodules is enabled on minions at any point and the
deployment server doesn't have the submodules checked out then the
minions will enter an unrecoverable state after the initial deploy.

This change always does a submodule recursive init for repos to
ensure this condition can't happen.

Change-Id: I125e9275d813dc34baed10878c19be94e4a0251e