A quick bash script to git-keep all subdirectories of the given directory by adding .gitkeep when no contents are present.

keep-everything.sh

#!/usr/bin/env bash
files_created=0

echo_usage()
{
    echo "Usage: keep-everything.sh /path/which/to/look/in"
    echo ""
}

echo_green()
{
    echo -e "\033[32m${1}\033[0m"
}

echo_red()
{
    echo -e "\033[31m${1}\033[0m"
}

traverse_directory()
{
    entries=0
    for d in "$1"/*
    do
        if [[ -d ${d} ]]; then
            traverse_directory ${d}
            entries=$((entries+1))
        elif [[ -f ${d} ]]; then
            entries=$((entries+1))
        fi
    done

    if [[ ${entries} == 0 ]]; then
        ignore_file="${1}/.gitignore"

        if [[ ! -f $ignore_file ]]; then
            touch ${ignore_file}
            echo_green "Created '${ignore_file}'"
            files_created=$((files_created + 1))
        fi
    fi
}

if [[ "${1}" == "" ]]; then
    echo_usage
    echo_red "ERROR: No path given!"
    exit
fi

if [[ ! -d ${1} || -r ${d} ]]; then
    echo_usage
    echo_red "ERROR: Directory not valid or not readable!"
    exit
fi

echo "Git-keeping all directories inside ${1}..."
traverse_directory $1
if [[ ${files_created} == 1 ]]; then
    echo_green "Created 1 .gitignore file"
else
    echo_green "Created ${files_created} .gitignore files"
fi
echo "All done!"

Doesn't check for hidden files (yet)