These scripts can be used to prune a Git repository down to just the contents of the specified subdirectory, and prunes the change history to only the files contained within.

git_filter_dir.bat

@echo off

setlocal enableextensions enabledelayedexpansion

set dir=%1
set dir=!dir:\=/!

git remote rm origin
git filter-branch --tag-name-filter cat --prune-empty --subdirectory-filter "%dir%" HEAD
git reset --hard
for /f %%r in ('git for-each-ref --format="%(refname)" refs/original/') do git update-ref -d %%r
git reflog expire --expire=now --all
git gc --aggressive --prune=now

git_filter_dir.sh

#!/bin/sh

git remote rm origin
git filter-branch --tag-name-filter cat --prune-empty --subdirectory-filter "$1" HEAD
git reset --hard
git for-each-ref --format="%(refname)" refs/original/ | xargs -n 1 git update-ref -d
git reflog expire --expire=now --all
git gc --aggressive --prune=now