Spurious modification reports from `next-status` about datalad-next HOT 4 CLOSED

Here is another one, seem the issues is "fixed" by an intermediate call to git diff (which reports an empty diff).

❯ git st
 modified: src/linkml/schemas/datalad-dataset-components.yaml (file)
untracked: src/examples/datalad-dataset.jsonld
❯ git st
 modified: src/linkml/schemas/datalad-dataset-components.yaml (file)
untracked: src/examples/datalad-dataset.jsonld
❯ git diff
❯ git st
untracked: src/examples/datalad-dataset.jsonld

from datalad-next.

I have a situation now, where I have a file open in vim. The file is in a plain Git repo, tracked, and has no modifications wrt to the committed state.

After I save the file in vim, no modifications, just :write, I see this "wrong" report.

❯ datalad next-status
 modified: src/examples/dataset-version/DatasetVersionObject-penguins.yaml (file)

The cause for this report is that git diff-index shows it too!

❯ git diff-index HEAD
:100644 100644 03657a3bf83d09a48060228feed6a70237ef4600 0000000000000000000000000000000000000000 M      src/examples/dataset-version/DatasetVersionObject-penguins.yaml

As soon as I run git diff or git status it is gone, as soon as I save the file in vim again, it is back:

❯ git diff
❯ git diff-index HEAD
❯ git diff-index HEAD
:100644 100644 03657a3bf83d09a48060228feed6a70237ef4600 0000000000000000000000000000000000000000 M      src/examples/dataset-version/DatasetVersionObject-penguins.yaml

from datalad-next.

https://stackoverflow.com/questions/34807971/why-does-git-diff-index-head-result-change-for-touched-files-after-git-diff-or-g has an explanation and possible mitigation strategy.

from datalad-next.

But there is more to this issue. I can do the exact same action (open README.md file in vim, make no change, but write it out again) in two different repos. I get the modification report on one repo (clone of https://github.com/psychoinformatics-de/datalad-concepts), but not another (clone of https://github.com/datalad/datalad-next).

from datalad-next.