One of my site git file became too big, and took long time to clone.
So I had to clean it.
git checkout --orphan latest_branch
2. Add all the files
git add -A
3. Commit the changes
git commit -am "commit message"
4. Delete the branch
git branch -D master
5. Rename the current branch to master
git branch -m master
6. Finally, force update your repository
git push -f origin master
To be a good house keeper.