git reset --hard can leave modified files

Thank you for filling out a Git bug report! Please answer the following questions to help us understand your issue.

What did you do before the bug happened? (Steps to reproduce your issue) git clone https://github.com/intel/llvm cd llvm git checkout git-bug-reproducer git merge 38df0bd4fccd1067f3abe078d42e94c740748628 -m Merge1 --no-ff git merge b6b8d34554a4d85ec064463b54a27e073c42beeb -m Merge2 --no-ff git reset --hard HEAD~ git status --porcelain

What did you expect to happen? (Expected behavior) An empty output from the last command

What happened instead? (Actual behavior)
 M clang-tools-extra/test/clang-apply-replacements/Inputs/crlf/crlf.cpp
 M clang-tools-extra/test/clang-apply-replacements/Inputs/crlf/crlf.cpp.expected

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

Anything else you want to add: The issue is flaky. First found for v2.29.2 Multiple executions of the "git reset --hard HEAD" can help. I ran a simple script to get some numbers: 100 attempts to get and fix the issue with up to 100 runs of the "git reset --hard HEAD" Got max number of runs - 45. Most of the cases (63) required 5 runs. 5 cases did not get the issue at all. V2.36.0 built from sources got similar results:

The script: (set -e; for a in {0..99}; do echo ++++++++++++++++ a=$a; git reset --hard origin/git-bug-reproducer; git merge b2d4d67d5e34c345cb6a3cf725b2e26a15a9dfe5 -m Merge1 --no-ff; git merge b6b8d34554a4d85ec064463b54a27e073c42beeb -m Merge2 --no-ff; git reset --hard HEAD~; for b in {1..99}; do git status --porcelain | grep . || break; git reset --hard HEAD; done; echo ++++++++ b=$b; git status --porcelain | grep . || continue; echo FAILED $a; break; done) > ../logg 2>&1

Please review the rest of the bug report below. You can delete any lines you don't wish to share.

[System Info] git version: git version 2.36.0 cpu: x86_64 no commit associated with this build sizeof-long: 8 sizeof-size_t: 8 shell-path: /bin/sh uname: Linux 4.18.0-193.el8.x86_64 #1 SMP Fri Mar 27 14:35:58 UTC 2020 x86_64 compiler info: gnuc: 4.4 libc info: glibc: 2.28 $SHELL (typically, interactive shell): /bin/bash

[Enabled Hooks] not run from a git repository - no hooks to show