Restore git submodules from .gitmodules. Since git submodule init only considers submodules that already are in the index (i.e. "staged") for initialization this short script parses .gitmodules, and each url and path pair.

restore-git-submodules.sh

#!/bin/sh

set -e

git config -f .gitmodules --get-regexp '^submodule\..*\.path$' |
    while read path_key path
    do
        url_key=$(echo $path_key | sed 's/\.path/.url/')
        url=$(git config -f .gitmodules --get "$url_key")
        git submodule add $url $path
    done