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Creating an empty commit in a new project
$ git clone <stash>/your_new_proj.git
$ cd your_new_proj
$ git commit -m "initial" --allow-empty
If you need to create a new parent with no files in an existing project (ie, you oops'd)
$ git clone <stash>/your_existing_proj.git
$ git checkout --orphan new_root
$ git reset --hard
$ git commit -m 'initial empty commit' --allow-empty
$ git checkout origin/master -b oldmaster
$ git rebase new_root
$ git push origin oldmaster:master -f