When you run git status , you see the screen below

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)
  (commit or discard the untracked or modified content in submodules)

    modified:   app (modified content, untracked content)
    modified:   lib (modified content, untracked content)

No mater how you add these files (git add *) , the files are still not being committed or staged.

Root cause: it’s because these folder has .git folder in side.
Fix: remove .git folder

find ./ -depth -mindepth 2 -type d -name .git -exec rm -rf \{\} \;