git checkout-index --all --force does not restore all files when `core.autocrlf` is set to `input`

git checkout-index --all --force does not restore all files when `core.autocrlf` is set to `input`

[Anthony Sottile]

I'm not sure if this is a bug or the intended behaviour.

Here's my minimal reproduction (using python3 to write files so I can
control line endings)

```
#!/bin/bash
set -ex

rm -rf repo
git init repo
cd repo

git config --local core.autocrlf input

python3 -c 'open("foo", "wb").write(b"1\r\n2\r\n")'
git add foo
python3 -c 'open("foo", "wb").write(b"3\r\n4\r\n")'

git checkout-index --all --force
echo 'I expect this `git status` to have no modifications'
git status
```

Here's the output:

```
+ rm -rf repo
+ git init repo
Initialized empty Git repository in /tmp/foo/repo/.git/
+ cd repo
+ git config --local core.autocrlf input
+ python3 -c 'open("foo", "wb").write(b"1\r\n2\r\n")'
+ git add foo
warning: CRLF will be replaced by LF in foo.
The file will have its original line endings in your working directory.
+ python3 -c 'open("foo", "wb").write(b"3\r\n4\r\n")'
+ git checkout-index --all --force
+ echo 'I expect this `git status` to have no modifications'
I expect this `git status` to have no modifications
+ git status
On branch master

Initial commit

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

    new file:   foo

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

    modified:   foo

```

In this state, `git diff` and `git diff-index` disagree as well:

```
$ git diff-index --exit-code $(git write-tree) --patch; echo $?
1
$ git diff --exit-code; echo $?
0
```

I expect the plumbing command `checkout-index -af` to exactly restore
the disk state to the index such that `git status`, and `git
diff-index` both indicate there are no changes.

Interestingly, `git checkout -- .` does exactly this, but it is a
porcelain command and not suitable for scripting.  Alternatively, I'm
looking for an equivalent to `git checkout -- .` which uses only
plumbing commands.

Thanks,

Anthony