2.3. Untracked Files - shinokada/gitnotes GitHub Wiki
While I was making dotfiles, I could not upload two directories, .oh-my-zsh and .zsh/zsh-syntax-highlighting. The reason was that they had .git folders. So I deleted .git and .gitignore. And cleared cache and add them all again.
$ cd ~/dofiles/.oh-my-zsh
$ rm -rf .git
$ rm .gitignore
$ cd ~/dofiles/.zsh/zsh-syntax-highlighting
$ rm -rf .git
$ rm .gitignore
$ cd ~/dotfiles
$ git rm -r --cached .
$ git add .
$ git commit -m "fixed untracked files"