Question

How can I cleanup git working file set (like hg up -r null)?

So only $proj/.git hierarchy present and git st don’t show D (deleted).

Answer 1

After clarifications in your comments, it seems that you want to create a new root commit in your repository. There’s a description of how to do this in the git community book.

First, make sure that the output of git status is clean, so that you don’t lose any of your previous work unintentionally. Then if you do the following:

git symbolic-ref HEAD refs/heads/newbranch 
rm .git/index 
git clean -fdx 
git commit --allow-empty -m 'Initial empty commit'

Then you will be on a new branch called newbranch, with a single root commit with an empty tree. If you then decide that you want this to be your new master branch, you can do:

git branch -m master oldmaster
git branch -m newbranch master

… which renames your old master branch to oldmaster, and then renames the new newbranch branch to master.