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How to Flatten the History of a Git Repository Safely
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

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