Bug: diff-index reports unrelated files as deleted when fsmonitor is enabled

git write-tree and then git diff-index reports thousands of files as `deleted` when core.fsmonitor is true, even though the files are still present on the file system.

What did you do before the bug happened? (Steps to reproduce your issue)

``` git config core.fsmonitor true touch new-file.txt git add new-file.txt git diff-index --ignore-submodules --exit-code --no-color --no-ext-diff $(git write-tree) -- ```

What did you expect to happen? (Expected behavior)

I expected that no files would be reported as having changes.

What happened instead? (Actual behavior)

Thousands of unrelated files were reported as `deleted`.

``` git diff-index --ignore-submodules --exit-code --no-color --no-ext-diff $(git write-tree) -- :100644 000000 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0000000000000000000000000000000000000000 D src/tests/__init__.py :100644 000000 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0000000000000000000000000000000000000000 D src/tests/site/__init__.py :100644 000000 d8edaad92120781998e811277f966551b12fc823 0000000000000000000000000000000000000000 D src/tests/site/test_models.py

 ... thousands of other files
```

What's different between what you expected and what actually happened?

Thousands of unrelated files were reported as having been deleted.

Anything else you want to add:

Myself and a few co-workers all ran into this issue in the last few days. It presented itself when pre-commit hooks were run (specifically with the pre-commit tool from github pre-commit).

When committing changes, the pre-commit tool runs the equivalent of:

`git diff-index --ignore-submodules --exit-code --no-color --no-ext-diff $(git write-tree) --`

It then stashes and unstashes those changes, causing the files to be removed from the working tree.

``` $ git config core.fsmonitor true $ git checkout -b test-branch Switched to a new branch 'test-branch'

$ echo "test 3" >> newfile.txt
$ git add .
$ git status
On branch test-branch
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
new file:   newfile.txt

$ git commit -a -m "will it fail?"
[WARNING] Unstaged files detected.
[INFO] Stashing unstaged files to
/Users/josh/.cache/pre-commit/patch1677888420-10129.
trim trailing whitespace.................................................Passed
check python ast.....................................(no files to check)Skipped
check for case conflicts.................................................Passed
[INFO] Restored changes from
/Users/josh/.cache/pre-commit/patch1677888420-10129.
[test-branch 7c899582c19] will it fail?
 1 file changed, 1 insertion(+)
 create mode 100644 newfile.txt

$ git status
On branch test-branch
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
deleted:    src/tests/__init__.py
deleted:    src/tests/site/__init__.py
deleted:    src/tests/site/test_models.py
        ... lots more files ...

no changes added to commit (use "git add" and/or "git commit -a")

$ git status | wc -l
   15298

$ git restore .

$ git status

On branch test-branch nothing to commit, working tree clean ```

It can be reproduced, in our repo, without using pre-commit at all:

```

git diff-index --ignore-submodules --exit-code --no-color --no-ext-diff $(git write-tree) -- :100644 000000 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0000000000000000000000000000000000000000 D src/tests/__init__.py :100644 000000 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0000000000000000000000000000000000000000 D src/tests/site/__init__.py :100644 000000 d8edaad92120781998e811277f966551b12fc823 0000000000000000000000000000000000000000 D src/tests/site/test_models.py

 ... thousands of other files
```

Using `update-index` with the `--no-fsmonitor` flag prior to diff-index does the correct thing:

``` $ git update-index --really-refresh --no-fsmonitor warning: core.fsmonitor is set; remove it if you really want to disable fsmonitor

$ git diff-index --ignore-submodules --exit-code --no-color --no-ext-diff $(git write-tree) --

```

The problem persists when running `update-index` without disabling fsmonitor.

I have reported this issue to the pre-commit project, but it looks like an issue with fsmonitor + write-tree.

See: pre-commit issues on github #2795

[System Info] git version: git version 2.39.2 (others reproduced with 2.39.1) cpu: arm64 no commit associated with this build sizeof-long: 8 sizeof-size_t: 8 shell-path: /bin/sh feature: fsmonitor--daemon uname: Darwin 22.3.0 Darwin Kernel Version 22.3.0: Mon Jan 30 20:38:37 PST 2023; root:xnu-8792.81.3~2/RELEASE_ARM64_T6000 arm64 compiler info: clang: 14.0.0 (clang-1400.0.29.202) libc info: no libc information available $SHELL (typically, interactive shell): /bin/zsh

[Enabled Hooks] pre-commit

Hi Josh,

On Sat, 4 Mar 2023, Josh Smeaton wrote:

I suspect that the issue is a missing `git update-index --refresh`. While `git diff` refreshes the index automatically, `git diff-index` does not (when you use low-level commands like `diff-index` you need to do such things explicitly).

If that does not fix your problem, I encourage you to distill the issue into a simple MCVE (https://stackoverflow.com/help/mcve), preferably in the form of a patch, say, to t7527 (see https://github.com/git/git/blob/v2.40.0/t/t7527-builtin-fsmonitor.sh).

Ciao, Johannes