Problem identified

Could not open /var/www/website/html/libraries/vendor/tobscure/json-api/.git/logs/HEAD for writing.

Prior to this error is I've been importing article contents manually via CSV. I wouldn't thought it would break Joomla! update by doing CSV import.

Any thought how to fix this issue? I also check the file that is mentioned in the error and it does exists. The file permission is also right (644). I also tried to upload a fresh copy of libraries folder from the Joomla! 4.1.0 update zip file but the error still appears. I did restore Joomla! core files several times before when I was working on my com_content custom override without an issue until I was importing articles to db manually.

Any help or hint how to fix it would be greatly appreciated and besides this might help other people who have this issue later on.

Thanks!