git read-tree

Alice/> git init
Initialized empty Git repository in /home/rene/github/github/git-internals/repos/read-tree/Alice/.git/

Alice/> echo one > one.txt

Alice/> mkdir dir; echo two > dir/two.txt

Alice/> mkdir dir/subdir; echo three > dir/subdir/three.txt

Alice/> git add *

Alice/> git commit . -m "added a few files"
[master (root-commit) b475e40] added a few files
 3 files changed, 3 insertions(+)
 create mode 100644 dir/subdir/three.txt
 create mode 100644 dir/two.txt
 create mode 100644 one.txt

Alice/> git rm -r dir
rm 'dir/subdir/three.txt'
rm 'dir/two.txt'

Alice/> git commit . -m "deleted a few files"
[master 267ef04] deleted a few files
 2 files changed, 2 deletions(-)
 delete mode 100644 dir/subdir/three.txt
 delete mode 100644 dir/two.txt

Alice/> git status
On branch master
nothing to commit, working directory clean

Alice/> git read-tree b475e40

Alice/> git status
On branch master
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	new file:   dir/subdir/three.txt
	new file:   dir/two.txt

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	deleted:    dir/subdir/three.txt
	deleted:    dir/two.txt