The root cause of this error in my case was that I have a subdirectory with its own .git folder inside. When I issued the git add --all command, I got this same error.

Here's how I resolved the issue:

  Remove all .git folder inside the sub directory causing the error

  cd to the main directory

  git rm --cached sub_directory_name -f

  git add --all to add the subdirectory and contents, recursively

  git status to verify that the items are added