Why doesn't git recognize that my file has been changed, therefore git add not working

Question

I am trying to push my files to github using bash. They are already on there, and I am uploading a newer version with new lines and code, etc. But when I try git add<

Answer 1

Ran into the issue, but it was only two directories and unknown to me was that both those directories ended up being configured as git submodules. How that happened I have no clue, but the process was to follow some of the instructions on this link, but NOT remove the directory (as he does at the end) but rather do git add path/to/dir