Please describe the problem.

git status reports having staged changes and no changes from index

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git status
On branch draft
Your branch is up to date with 'github/draft'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   .dandi/assets.json

no changes added to commit (use "git add" and/or "git commit -a")

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git annex status
M ./.dandi/assets.json

although git shows no diff and sha256 checksum corresponds to the key:

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git diff --cached
(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git show -- .dandi/assets.json
commit b859efed7ddb2ff31cc26168f40676c572d2798f (HEAD -> draft, github/draft, github/HEAD)
Author: DANDI User <>
Date:   Fri Sep 16 22:22:29 2022 +0000

    [backups2datalad] 66 files added

diff --git a/.dandi/assets.json b/.dandi/assets.json
index d3ef95e1ee..62fe372810 100644
--- a/.dandi/assets.json
+++ b/.dandi/assets.json
@@ -1 +1 @@
(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ sha256sum .dandi/assets.json
6a0a91c4158d316ab8ad9bd8ebf7579b9c3c579e1035c48134246b6a5d2f6f14  .dandi/assets.json

I think may be the tricky part is that I have it of

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git config annex.version

although I thought that we kept it at 8 but I have user wider config setting

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git config filter.annex.process
git-annex filter-process

I was recommended to speed up operations while avoiding upgrade to 10, but I guess running most recent version once lead to the upgrade since all the other repos are still at 8 as I thought it would be

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ grep -h '\<version =' ../*/.git/config | sort | uniq -c
      1         version = 10
    186         version = 8

having it reported modified causes our script which does sanity check to operate only on clean repo to fail.

git reset --hard seems mitigated that

(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git reset --hard
HEAD is now at b859efed7d [backups2datalad] 66 files added
(git-annex) dandi@drogon:/mnt/backup/dandi/dandisets/000026$ git status
On branch draft
Your branch is up to date with 'github/draft'.

nothing to commit, working tree clean

all. I will now rerun our script and see in what state I would end up (although, once again, I ended up in version 10 of the repo already, so may be behavior would be different).

What steps will reproduce the problem?

I think I get it after I annex move and then annex get that file back. Just for my own reference -- git-annex repo is result of the

What version of git-annex are you using? On what operating system?

10.20220822-g84f1875 (conda build), originally observed on earlier 10.20220724-ge30d846

fixed --Joey