Can't checkout because files were "changed" (they're unchanged, but made on Linux), commit didn't fix

[makssem13]

Existing issues matching what you're seeing

• I was not able to find an open or closed issue matching what I'm seeing

Git for Windows version

git version 2.52.0.windows.1
cpu: x86_64
built from commit: 2912d8e9b8253723974b7baf1c890273b1a1c5bd
sizeof-long: 4
sizeof-size_t: 8
shell-path: D:/git-sdk-64-build-installers/usr/bin/sh
rust: disabled
feature: fsmonitor--daemon
libcurl: 8.17.0
OpenSSL: OpenSSL 3.5.4 30 Sep 2025
zlib: 1.3.1
SHA-1: SHA1_DC
SHA-256: SHA256_BLK
default-ref-format: files
default-hash: sha1

Windows version

Windows 11

Windows CPU architecture

x86_64 (64-bit)

Additional Windows version information

Microsoft Windows [Version 10.0.26200.7623]

Options set during installation

Editor Option: VIM
Custom Editor Path:
Default Branch Option:
Path Option: Cmd
SSH Option: OpenSSH
Tortoise Option: false
CURL Option: OpenSSL
CRLF Option: CRLFAlways
Bash Terminal Option: MinTTY
Git Pull Behavior Option: Merge
Use Credential Manager: Enabled
Performance Tweaks FSCache: Enabled
Enable Symlinks: Disabled
Enable FSMonitor: Disabled

Other interesting things

None

Terminal/shell

cmd

Commands that trigger the issue

git checkout v2.6.39

Expected behaviour

change the code to what was back in time at v2.6.39 marker

Actual behaviour

error about "changed files" (they're untouched except of my new file, but it was commited (I'm too lazy for searching what is stashing, it's all for experimenting)):
D:\msys64\home\Maks\test\linux>git commit -a -m "pls work"
[master 3fcccfbcdcfc] pls work
1 file changed, 41 insertions(+)
create mode 100644 git-bugreport-2026-01-24-2148.txt

D:\msys64\home\Maks\test\linux>git checkout v2.6.39
error: Your local changes to the following files would be overwritten by checkout:
include/uapi/linux/netfilter/xt_CONNMARK.h
include/uapi/linux/netfilter/xt_DSCP.h
include/uapi/linux/netfilter/xt_MARK.h
include/uapi/linux/netfilter/xt_RATEEST.h
include/uapi/linux/netfilter/xt_TCPMSS.h
include/uapi/linux/netfilter_ipv4/ipt_ECN.h
include/uapi/linux/netfilter_ipv4/ipt_TTL.h
include/uapi/linux/netfilter_ipv6/ip6t_HL.h
net/netfilter/xt_DSCP.c
net/netfilter/xt_HL.c
net/netfilter/xt_RATEEST.c
net/netfilter/xt_TCPMSS.c
tools/memory-model/litmus-tests/Z6.0+pooncelock+poonceLock+pombonce.litmus
Please commit your changes or stash them before you switch branches.
Aborting

Repository

https://github.com/torvalds/linux

[smacdonald-kai]

You're probably running into end-of-line differences; LF for *nix and CRLF for WIndows.

[tboegi]

Probably: You are cloning a repo with filenames that differ only in case
onto a filesystem which can not handle it because it is case insensitive.
Did you get a warning about file name collision(s) (or similar) ?