Add files
git add -A stages All
git add . stages new and modified, without deleted
git add -u stages modified and deleted, without new
Remove directory from git and local
git rm -r one-of-the-directories
git commit -m "Remove duplicated directory"
git push origin <your-git-branch> (typically 'master', but not always)
Remove directory from git but NOT local
What you usually want to do is remove this directory from git but not delete it entirely from the filesystem (local).
git rm -r --cached myFolder
Commit
git init
git add .
git commit -m "First commit"
git remote add origin remote repository URL
git remote -v
git push origin master