Git re-creates newly added directory when it is pushed

I create a new directory, add it to git and push it.

After push it says: Unable to read current working directory: No such file or directory

[yuri@yv /usr/ports/math/stanmath]$ git pull -r && git push origin 
--push-option=confirm-author
remote: Enumerating objects: 283, done.
remote: Counting objects: 100% (283/283), done.
remote: Compressing objects: 100% (187/187), done.
remote: Total 188 (delta 94), reused 3 (delta 0), pack-reused 0
Receiving objects: 100% (188/188), 29.37 KiB | 578.00 KiB/s, done.
Resolving deltas: 100% (94/94), completed with 50 local objects.
 From ssh://gitrepo.freebsd.org/ports
    80469139f77f..cf8b94761057  main       -> origin/main
Successfully rebased and updated refs/heads/main.
fatal: Unable to read current working directory: No such file or directory

Why does Git have to delete and then create again the directory when it is already there?

This isn't a big issue, but it is very odd that git deletes the working directory.

FreeBSD 13.

Yuri