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### Please describe the problem.
I have a repository that contains thousands (30000) of unlocked files. I see the problem that
git keeps refreshing its index despite the modified time did not change compared to the git index.
I think this should not happen. It significantly slows down (delay of ~10s in my case, but
potentially worse for Windows or NFS file systems) any git operation, and this includes
the display of a bash prompt that shows git information (via PROMPT_COMMAND env var.) and bash
completion after things like `git add`, therefore it is quite annoying.
### What steps will reproduce the problem?
I have set up a repository to reproduce the problem. However, it works as expected. I am looking for
ideas on how to find the problem with my repository.
```
git init .
git annex init
git annex config --set annex.addunlocked include="py_env/*"
python -m venv py_env
. py_env/bin/activate
pip install datalad # some package with dependencies that creates many files in py_env
git annex add py_env
git status
git status
git status
...
```
The only strange thing that I have found is that git annex will forward all `__init__.py` files to the smudge/clean-filter (pipes to filter-process), but only those! It does not do this for all other files in `py_env`, as you can check with
```sh
strace git status 2>&1 | grep "^write.*pathname="
```
this shows only the `__init__.py` files, despite `find py_env` shows many more files in there and they are skipped. I think that git skips files during `git status` if the mtime and the ctime are the same. But they are always the same, as can be checked by comparing
```sh
git ls-files --debug "(any file that shows up in strace)"
stat -c $'ctime: %.9Z\nmtime: %.9Y' "(same file)"
```
I do not know how to debug further and are grateful for suggestions!
### What version of git-annex are you using? On what operating system?
git-annex version: 10.20250115-ga55e1da1aa0eb07b418e899cc200027e082eb82a
git version 2.47.1
Rocky Linux
### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)