How to Flatten the History of a Git Repository Safely

gistfile1.md

git checkout --orphan future-master
git add -A  # Add all files and commit them
git commit
git branch -D master  # Deletes the master branch
git branch -m master  # Rename the current branch to master
git push -f origin master  # Force push master branch to github
git gc --aggressive --prune=all     # remove the old files

Works well with git submodules too. From: https://stackoverflow.com/a/13102849/1253966