checkout: incorrectly states files are modified when they are executable

[jldorscheidt]

Bug Report

checkout: incorrectly states files are modified when they are executable

Description

When tracking a file that is executable, using a shared cache with symlinks, dvc checkout keeps stating changes are applied to the file.

Reproduce

contents of dvc.yaml:

  stages:
    add_some_text:
      wdir: ../
      desc: write some text
      cmd:
        - > 
          touch data/some_new_file.txt
      deps:
        - data/data.txt
      outs:
        - data/some_new_file.txt

contents of config

[cache]
    dir = ../../cache
    type = symlink
    shared = group
['remote "temp"']
    url = ../../remote
[core]
    remote = temp

steps to reproduce:

1. mkdir -p dvc_mwe/dvc_mwe/data dvc_mwe/cache dvc_mwe/remote
2. touch dvc_mwe/dvc_mwe/data/data.txt && chmod +x dvc_mwe/dvc_mwe/data/data.txt
3. cd dvc_mwe/dvc_mwe
4. git init && dvc init
5. Copy contents of dvc.yaml to dvc_mwe/dvc_mwe/data/dvc.yaml
6. Copy contents of config to dvc_mwe/dvc_mwe/.dvc/config
7. dvc add data/data.txt
8. dvc repro data/dvc.yaml
9. dvc push
10. dvc checkout
11. dvc checkout

dvc checkout will keep stating that some_new_file.txt has been modified

Expected

repeatedly calling dvc checkout without any data changes should not print any files that have been modified

Environment information

python==3.10.12
dvc==3.55.2

Output of dvc doctor:

$ dvc doctor
DVC version: 3.55.2 (pip)
-------------------------
Platform: Python 3.10.13 on Linux-6.9.3-76060903-generic-x86_64-with-glibc2.35
Subprojects:
	dvc_data = 3.16.6
	dvc_objects = 5.1.0
	dvc_render = 1.0.2
	dvc_task = 0.40.2
	scmrepo = 3.3.8
Supports:
	http (aiohttp = 3.10.10, aiohttp-retry = 2.8.3),
	https (aiohttp = 3.10.10, aiohttp-retry = 2.8.3)
Config:
	Global: /home/joostdorscheidt/.config/dvc
	System: /etc/xdg/xdg-pop/dvc
Cache types: hardlink, symlink
Cache directory: ext4 on /dev/mapper/data-root
Caches: local
Remotes: local
Workspace directory: ext4 on /dev/mapper/data-root
Repo: dvc, git
Repo.site_cache_dir: /var/tmp/dvc/repo/8324f5dfe498694db375810644b6aa5a

Additional Information (if any):

[robince]

I see the same behaviour with files with executable bit set in a tracked folder. The folder is listed as modified on every pull or checkout. Removing the executable permission on all the files stopped this.

DVC version: 3.58.0 (brew)
--------------------------
Platform: Python 3.13.0 on macOS-14.7.1-arm64-arm-64bit-Mach-O
Subprojects:
	dvc_data = 3.16.7
	dvc_objects = 5.1.0
	dvc_render = 1.0.2
	dvc_task = 0.40.2
	scmrepo = 3.3.9
Supports:
	azure (adlfs = 2024.7.0, knack = 0.12.0, azure-identity = 1.19.0),
	gdrive (pydrive2 = 1.21.3),
	gs (gcsfs = 2024.10.0),
	hdfs (fsspec = 2024.10.0, pyarrow = 18.1.0),
	http (aiohttp = 3.11.8, aiohttp-retry = 2.9.1),
	https (aiohttp = 3.11.8, aiohttp-retry = 2.9.1),
	oss (ossfs = 2023.12.0),
	s3 (s3fs = 2024.10.0, boto3 = 1.35.36),
	ssh (sshfs = 2024.9.0),
	webdav (webdav4 = 0.10.0),
	webdavs (webdav4 = 0.10.0),
	webhdfs (fsspec = 2024.10.0)
Config:
	Global: /Users/user/Library/Application Support/dvc
	System: /opt/homebrew/share/dvc
Cache types: reflink, hardlink, symlink
Cache directory: apfs on /dev/disk3s1s1
Caches: local
Remotes: azure
Workspace directory: apfs on /dev/disk3s1s1
Repo: dvc, git
Repo.site_cache_dir: /opt/homebrew/var/cache/dvc/repo/1f3fb65063a5abf9859cedb42ce3cc1f