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    <p>Expanding on @Mark Longair's answer, I wrote a bash script to automate steps 2 &amp; 3 of the following process:</p> <ol> <li>Clone a 'boilerplate' repo to begin a new project</li> <li>Remove the .git folder and re-initialize as a new repo</li> <li>Re-initialize the submodules, prompting for input before deleting folders</li> </ol> <hr> <pre><code>#!/bin/bash set -e rm -rf .git git init git config -f .gitmodules --get-regexp '^submodule\..*\.path$' &gt; tempfile while read -u 3 path_key path do url_key=$(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&lt;tempfile rm tempfile </code></pre> <p><em>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.</em></p> <p>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 :)</p> <hr> <p>Big thanks to Mark, <a href="https://stackoverflow.com/a/226724/193494">https://stackoverflow.com/a/226724/193494</a>, <a href="https://stackoverflow.com/q/11704353/193494">bash: nested interactive read within a loop that&#39;s also using read</a>, and tnettenba @ chat.freenode.net for helping me arrive at this solution!</p>
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