If you have more than 30 Repositories, the original script will not download all. The github api limits the entries to 30 per page but you can raise that up to 100. I have added a small loop which sets the limit to 90 and cycles through all pages until the listing on a page is empty...

backup-github.sh

#!/bin/bash
# A simple script to backup an organization's GitHub repositories.

TSTAMP=$(date +%Y-%m-%d_%H-%M-%S)
GHBU_BACKUP_DIR=${TSTAMP}                                            # where to place the backup files
GHBU_ORG_TYPE=${GHBU_ORG_TYPE-"<CHANGE-ME>"}                         # are you doing an organization or a user (orgs | users)
GHBU_ORG=${GHBU_ORG-"<CHANGE-ME>"}                                   # the GitHub organization (or GitHub username) whose repos will be backed up
GHBU_UNAME=${GHBU_UNAME-"<CHANGE-ME>"}                               # the username of a GitHub account (to use with the GitHub API)
GHBU_PASSWD=${GHBU_PASSWD-"<CHANGE-ME>"}                             # the password for that account
GHBU_GITHOST=${GHBU_GITHOST-"github.com"}                            # the GitHub hostname (see notes)
GHBU_PRUNE_OLD=${GHBU_PRUNE_OLD-true}                                # when `true`, old backups will be deleted
GHBU_PRUNE_AFTER_N_DAYS=${GHBU_PRUNE_AFTER_N_DAYS-3}                 # the min age (in days) of backup files to delete
GHBU_SILENT=${GHBU_SILENT-false}                                     # when `true`, only show error messages
GHBU_API=${GHBU_API-"https://api.github.com"}                        # base URI for the GitHub API
GHBU_GIT_CLONE_CMD="git clone --quiet --mirror git@${GHBU_GITHOST}:" # base command to use to clone GitHub repos

# time stamp the files
TSTAMP=$(date "+%Y%m%d-%H%M")

# The function `check` will exit the script if the given command fails.
function check {
  "$@"
  status=$?
  if [ $status -ne 0 ]; then
    echo "ERROR: Encountered error (${status}) while running the following:" >&2
    echo "           $*"  >&2
    echo "       (at line ${BASH_LINENO[0]} of file $0.)"  >&2
    echo "       Aborting." >&2
    exit $status
  fi
}

# The function `tgz` will create a gzipped tar archive of the specified file ($1) and then remove the original
# the option -P omits the error message tar: Removing leading '/' from member names
function tgz {
   check tar zcPf "$1.tar.gz" "$1" && check rm -rf "$1"
}

echo "-------------"
echo "Date: $(date)"
echo "-------------"

$GHBU_SILENT || (echo "" && echo "=== INITIALIZING ===" && echo "")

$GHBU_SILENT || echo "Using backup directory $GHBU_BACKUP_DIR"
check mkdir -p "$GHBU_BACKUP_DIR"

$GHBU_SILENT || echo "Fetching list of repositories for ${GHBU_ORG}..."
# If you have more than 100 repositories, you'll need to step thru the list of repos
# returned by GitHub one page at a time.
# Cycling through pages:
PAGE=0
while true; do
  let PAGE++
  $GHBU_SILENT || echo "getting page ${PAGE}"
  REPOLIST_TMP=$(check curl --silent -u "$GHBU_UNAME:$GHBU_PASSWD" "${GHBU_API}/${GHBU_ORG_TYPE}/${GHBU_ORG}/repos?page=${PAGE}&per_page=90" -q -k | grep "\"name\"" | awk -F': "' '{print $2}' | sed -e 's/",//g')
  if [ -z "${REPOLIST_TMP}" ]; then break; fi
  REPOLIST="${REPOLIST} ${REPOLIST_TMP}"
done

list_count=$(echo "$REPOLIST" | wc -w)
list_count="$(echo -e "${list_count}" | tr -d '[:space:]')"
$GHBU_SILENT || echo "found $list_count repositories."


$GHBU_SILENT || (echo "" && echo "=== BACKING UP ===" && echo "")

# If you just want one, uncomment this line:
# REPOLIST="your-repo"
COUNT=0
for REPO in $REPOLIST; do
   let COUNT++
   current_repo=${REPO}
   echo
   echo "#$COUNT of $list_count: $current_repo"
   echo

   $GHBU_SILENT || echo "Backing up ${GHBU_ORG}/${REPO}"
   check ${GHBU_GIT_CLONE_CMD}${GHBU_ORG}/${REPO}.git ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}-${TSTAMP}.git && tgz ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}-${TSTAMP}.git
   sleep 5

   $GHBU_SILENT || echo "Backing up ${GHBU_ORG}/${REPO}.wiki (if any)"
   ${GHBU_GIT_CLONE_CMD}${GHBU_ORG}/${REPO}.wiki.git ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.wiki-${TSTAMP}.git 2>/dev/null && tgz ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.wiki-${TSTAMP}.git
   sleep 5

   $GHBU_SILENT || echo "Backing up ${GHBU_ORG}/${REPO} issues"
   check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/repos/${GHBU_ORG}/${REPO}/issues -q > ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.issues-${TSTAMP}.json && tgz ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.issues-${TSTAMP}.json
   sleep 5
done

if $GHBU_PRUNE_OLD; then
  $GHBU_SILENT || (echo "" && echo "=== PRUNING ===" && echo "")
  $GHBU_SILENT || echo "Pruning backup files ${GHBU_PRUNE_AFTER_N_DAYS} days old or older."
  $GHBU_SILENT || echo "Found $(find "$GHBU_BACKUP_DIR" -name '*.tar.gz' -mtime +"$GHBU_PRUNE_AFTER_N_DAYS" | wc -l) files to prune."
  find "$GHBU_BACKUP_DIR" -name '*.tar.gz' -mtime +"$GHBU_PRUNE_AFTER_N_DAYS" -exec rm -fv {} > /dev/null \;
fi

$GHBU_SILENT || (echo "" && echo "=== DONE ===" && echo "")
$GHBU_SILENT || (echo "GitHub backup completed." && echo "")

echo "-------------"
echo "Date: $(date)"
echo "-------------"

Restoring backups

1. un-tar the file
2. go into the directory
3. do a git push --mirror https://github.com/YOUR-ORG/YOUR-REPO.git