Restore git submodules from .gitmodules

I have a folder, which was a git repo. It contains some files and .gitmodules file. Now, when I do git init and then git submodule init, the latter command output is nothing. How can I help git to see submodules, defined in .gitmodules file without running git submodule add by hand again?

Update: this is my .gitmodules file:

[submodule "vim-pathogen"]
    path = vim-pathogen
    url = git://github.com/tpope/vim-pathogen.git
[submodule "bundle/python-mode"]
    path = bundle/python-mode
    url = git://github.com/klen/python-mode.git
[submodule "bundle/vim-fugitive"]
    path = bundle/vim-fugitive
    url = git://github.com/tpope/vim-fugitive.git
[submodule "bundle/ctrlp.vim"]
    path = bundle/ctrlp.vim
    url = git://github.com/kien/ctrlp.vim.git
[submodule "bundle/vim-tomorrow-theme"]
    path = bundle/vim-tomorrow-theme
    url = git://github.com/chriskempson/vim-tomorrow-theme.git

and here is listing of this dir:

drwxr-xr-x  4 evgeniuz 100 4096 июня  29 12:06 .
drwx------ 60 evgeniuz 100 4096 июня  29 11:43 ..
drwxr-xr-x  2 evgeniuz 100 4096 июня  29 10:03 autoload
drwxr-xr-x  7 evgeniuz 100 4096 июня  29 12:13 .git
-rw-r--r--  1 evgeniuz 100  542 июня  29 11:45 .gitmodules
-rw-r--r--  1 evgeniuz 100  243 июня  29 11:18 .vimrc

so, definitely, it is in top level. the git directory is not changed, only git init is done

git submodule init only considers submodules that already are in the index (i.e. "staged") for initialization. I would write a short script that parses .gitmodules, and for each url and path pair runs:

git submodule add <url> <path>

For example, you could use the following script:

#!/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

This is based on how the git-submodule.sh script itself parses the .gitmodules file.

Expanding on @Mark Longair's answer, I wrote a bash script to automate steps 2 & 3 of the following process:

1. Clone a 'boilerplate' repo to begin a new project
2. Remove the .git folder and re-initialize as a new repo
3. Re-initialize the submodules, prompting for input before deleting folders

#!/bin/bash

set -e
rm -rf .git
git init

git config -f .gitmodules --get-regexp '^submodule\..*\.path$' > tempfile

while read -u 3 path_key path
do
    url_key=$(echo $path_key | sed 's/\.path/.url/')
    url=$(git config -f .gitmodules --get "$url_key")

    read -p "Are you sure you want to delete $path and re-initialize as a new submodule? " yn
    case $yn in
        [Yy]* ) rm -rf $path; git submodule add $url $path; echo "$path has been initialized";;
        [Nn]* ) exit;;
        * ) echo "Please answer yes or no.";;
    esac

done 3<tempfile

rm tempfile

Note: the submodules will be checked out at the tip of their master branch instead of the same commit as the boilerplate repo, so you'll need to do that manually.

Piping the output from git config into the read loop was causing problems with the prompt for input, so it outputs it to a temp file instead. Any improvements on my first bash script would be very welcome :)

Big thanks to Mark, https://stackoverflow.com/a/226724/193494, bash: nested interactive read within a loop that's also using read, and tnettenba @ chat.freenode.net for helping me arrive at this solution!

Extending excellent @Mark Longair's answer to add submodule respecting branch and repo name.

#!/bin/sh

set -e

git config -f .gitmodules --get-regexp '^submodule\..*\.path$' |
    while read path_key path
    do
        name=$(echo $path_key | sed 's/\submodule\.\(.*\)\.path/\1/')
        url_key=$(echo $path_key | sed 's/\.path/.url/')
        branch_key=$(echo $path_key | sed 's/\.path/.branch/')
        url=$(git config -f .gitmodules --get "$url_key")
        branch=$(git config -f .gitmodules --get "$branch_key" || echo "master")
        git submodule add -b $branch --name $name $url $path || continue
    done