Repository: pre-commit/pre-commit
Issue: pre-commit can delete/revert unstaged files if error occurs during git diff-index

### search you tried in the issue tracker

diff-index

### describe your issue

I performed a git commit with some modifications unstaged.  After the commit, most of the modifications had been reverted and my work was lost.  The diff saved in the patch directory had only a few of the modifications in - the ones that survived. The rest were gone.

To reproduce:
- Modify four files and stage one with `git add`
- Use `git status` to determine the order of the three unstaged files.
- Change the permission on the middle one so that git will not be able to read it
- Now do `git commit`: the changes to the first unstaged file will be preserved but the other two will be lost.

The key point, I think, is that the code in `staged_files_only.py` checks that the return code when creating the diff is non-zero which it takes to mean that the code is `1` meaning that there were diffs.   However, in this case the return code is `128` which *is* non-zero but does _not_ mean success - it means error.  So the code assumes the diff is OK even though it is incomplete.

### pre-commit --version

2.17.0

### .pre-commit-config.yaml

```yaml
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
  rev: 56b4a7e506901ff86f8de5c2551bc41f8eacf717
  hooks:
     -   id: check-yaml
#     -   id: end-of-file-fixer
     -   id: trailing-whitespace
- repo: https://github.com/psf/black
  rev: 21.11b0
  hooks:
    -   id: black
        language_version: python3.6
- repo: https://github.com/PyCQA/isort
  rev: 5.10.1
  hooks:
    -   id: isort
        args: ["--profile", "black", "--filter-files"]
```


### ~/.cache/pre-commit/pre-commit.log (if present)

_No response_

Changed files:
pre_commit/staged_files_only.py, tests/staged_files_only_test.py

diff --git a/pre_commit/staged_files_only.py b/pre_commit/staged_files_only.py
index 172fb20..8812356 100644
--- a/pre_commit/staged_files_only.py
+++ b/pre_commit/staged_files_only.py
@@ -7,6 +7,7 @@ import time
 from typing import Generator
 
 from pre_commit import git
+from pre_commit.errors import FatalError
 from pre_commit.util import CalledProcessError
 from pre_commit.util import cmd_output
 from pre_commit.util import cmd_output_b
@@ -49,12 +50,16 @@ def _intent_to_add_cleared() -> Generator[None, None, None]:
 @contextlib.contextmanager
 def _unstaged_changes_cleared(patch_dir: str) -> Generator[None, None, None]:
     tree = cmd_output('git', 'write-tree')[1].strip()
-    retcode, diff_stdout_binary, _ = cmd_output_b(
+    diff_cmd = (
         'git', 'diff-index', '--ignore-submodules', '--binary',
         '--exit-code', '--no-color', '--no-ext-diff', tree, '--',
-        check=False,
     )
-    if retcode and diff_stdout_binary.strip():
+    retcode, diff_stdout, diff_stderr = cmd_output_b(*diff_cmd, check=False)
+    if retcode == 0:
+        # There weren't any staged files so we don't need to do anything
+        # special
+        yield
+    elif retcode == 1 and diff_stdout.strip():
         patch_filename = f'patch{int(time.time())}-{os.getpid()}'
         patch_filename = os.path.join(patch_dir, patch_filename)
         logger.warning('Unstaged files detected.')
@@ -62,7 +67,7 @@ def _unstaged_changes_cleared(patch_dir: str) -> Generator[None, None, None]:
         # Save the current unstaged changes as a patch
         os.makedirs(patch_dir, exist_ok=True)
         with open(patch_filename, 'wb') as patch_file:
-            patch_file.write(diff_stdout_binary)
+            patch_file.write(diff_stdout)
 
         # prevent recursive post-checkout hooks (#1418)
         no_checkout_env = dict(os.environ, _PRE_COMMIT_SKIP_POST_CHECKOUT='1')
@@ -86,10 +91,12 @@ def _unstaged_changes_cleared(patch_dir: str) -> Generator[None, None, None]:
                 _git_apply(patch_filename)
 
             logger.info(f'Restored changes from {patch_filename}.')
-    else:
-        # There weren't any staged files so we don't need to do anything
-        # special
-        yield
+    else:  # pragma: win32 no cover
+        # some error occurred while requesting the diff
+        e = CalledProcessError(retcode, diff_cmd, b'', diff_stderr)
+        raise FatalError(
+            f'pre-commit failed to diff -- perhaps due to permissions?\\n\\n{e}',
+        )
 
 
 @contextlib.contextmanager
diff --git a/tests/staged_files_only_test.py b/tests/staged_files_only_test.py
index a91f315..50f146b 100644
--- a/tests/staged_files_only_test.py
+++ b/tests/staged_files_only_test.py
@@ -1,12 +1,15 @@
 from __future__ import annotations
 
+import contextlib
 import itertools
 import os.path
 import shutil
 
 import pytest
+import re_assert
 
 from pre_commit import git
+from pre_commit.errors import FatalError
 from pre_commit.staged_files_only import staged_files_only
 from pre_commit.util import cmd_output
 from testing.auto_namedtuple import auto_namedtuple
@@ -14,6 +17,7 @@ from testing.fixtures import git_dir
 from testing.util import cwd
 from testing.util import get_resource_path
 from testing.util import git_commit
+from testing.util import xfailif_windows
 
 
 FOO_CONTENTS = '\\n'.join(('1', '2', '3', '4', '5', '6', '7', '8', ''))
@@ -382,3 +386,51 @@ def test_intent_to_add(in_git_dir, patch_dir):
     with staged_files_only(patch_dir):
         assert_no_diff()
     assert git.intent_to_add_files() == ['foo']
+
+
+@contextlib.contextmanager
+def _unreadable(f):
+    orig = os.stat(f).st_mode
+    os.chmod(f, 0o000)
+    try:
+        yield
+    finally:
+        os.chmod(f, orig)
+
+
+@xfailif_windows  # pragma: win32 no cover
+def test_failed_diff_does_not_discard_changes(in_git_dir, patch_dir):
+    # stage 3 files
+    for i in range(3):
+        with open(str(i), 'w') as f:
+            f.write(str(i))
+    cmd_output('git', 'add', '0', '1', '2')
+
+    # modify all of their contents
+    for i in range(3):
+        with open(str(i), 'w') as f:
+            f.write('new contents')
+
+    with _unreadable('1'):
+        with pytest.raises(FatalError) as excinfo:
+            with staged_files_only(patch_dir):
+                raise AssertionError('should have errored on enter')
+
+    # the diff command failed to produce a diff of `1`
+    msg, = excinfo.value.args
+    re_assert.Matches(
+        r'^pre-commit failed to diff -- perhaps due to permissions\\?\\n\\n'
+        r'command: .*\\n'
+        r'return code: 128\\n'
+        r'stdout: \\(none\\)\\n'
+        r'stderr:\\n'
+        r'    error: open\\("1"\\): Permission denied\\n'
+        r'    fatal: cannot hash 1\\n'
+        # TODO: not sure why there's weird whitespace here
+        r'    $',
+    ).assert_matches(msg)
+
+    # even though it errored, the unstaged changes should still be present
+    for i in range(3):
+        with open(str(i)) as f:
+            assert f.read() == 'new contents'