Bug? git commit fileA tries to delete fileB and other oddities

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Hi,

I have the following problems with a local repository:

* git commit fileA tries to delete fileX (fileX still exists).

* git restore --staged fileX doesn't work, the file remains staged.

* A commit from a few days back deleted 2 random files that I haven't
touched or staged in months and pulled in staged changes I didn't ask
for.

git version: 2.24.0 and 2.24.1 (OS: FreeBSD 12)

How can this happen? The repository has a local remote (on the same
filesystem) that is pushed to only. I tarred the project and copied it
to a Mac with git 2.23.0 and the problem persists.

For example (I've only changed the filenames):

% git status
On branch master
Your branch is up to date with 'origin/master'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        modified:   fileA
        modified:   fileB
        modified:   fileC

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


% git commit fileA

# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
#
# On branch master
# Your branch is up to date with 'origin/master'.
#
# Changes to be committed:
#       deleted:    fileX
#       modified:   fileA
#
# Changes not staged for commit:


% git stash
Saved working directory and index state WIP on master: 488e7081 ...


% git status
On branch master
Your branch is up to date with 'origin/master'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        deleted:    fileX

Untracked files:


% git restore --staged fileX


% git status
On branch master
Your branch is up to date with 'origin/master'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        deleted:    fileX

Untracked files:
  (use "git add <file>..." to include in what will be committed)


Thanks,
Mikael



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