merge_git.bash

#!/bin/bash

function avoid_conflict {
  if [ -f "$1" ]; then
    git checkout "$2"
    git mv "$1" "$3/"
    git commit -am 'Move file into subdirectory.'
  fi
}

function base {
  basename "$1" .git
}

function clone {
  [ -d $(base "$1") ] || git clone -b "$2" "$1"
}

function clone_branches {
  for branch in $(git branch -r | grep -vw -- '->'); do
    [ "$branch" = "origin/$1" ] || git checkout --track "$branch"
  done
}

function push_down {
  git filter-branch -f --prune-empty --tree-filter "mkdir .tmp;
    mv * .tmp;
    mv .tmp \"$1\"
    " -- --glob='refs/heads/*'
}

function track_branches {
  for branch in $(git branch -r | grep -vw -- '->'); do
    git checkout -b "$branch" --track "$branch"
  done
}

#
# New super repo
parent='path/to/parent.git'

parent_branch=master

#
# Old silo repos
children='path/to/first/child.git
path/to/second/child.git'

child_branch=master

#
# Clone all repos at the same level
clone "$parent" "$parent_branch"

for child in $children; do
  clone "$child" "$child_branch"
done

#
# Create the child directory and push content down one level
for child in $children; do
  proj=$(base "$child")

  cd "$proj"
  clone_branches "$child_branch"
  push_down "$proj"

  #
  # Prevent conflicts
  avoid_conflict .gitignore "$child_branch" "$proj"
  avoid_conflict .pairs "$child_branch" "$proj"

  git gc --aggressive
  cd -
done

path="$(pwd)"
cd $(base "$parent")

#
# Add the local repos to the new parent
for child in $children; do
  proj=$(base "$child")

  git remote add "$proj" "$path/$proj"
done

git fetch --all
track_branches
git checkout "$parent_branch"

for child in $children; do
  proj=$(base "$child")

  git merge --no-edit "$proj/$child_branch"
  git remote rm "$proj"
done

#
# The new parent is ready for action
git gc --aggressive
git push --all

Attempt at reusing logic from http://stackoverflow.com/questions/15477379/merge-two-git-repos-into-one-without-renaming-files/15517913#15517913.