Make “ArduinoProjects” repository first at github

 cd Arduino/
 echo "#Arduino Projects" >>README.md
 git init
 git add *
 git commit -m "first commit"
 git remote add origin git@github.com:<user>/ArduinoProjects.git
 git push --all origin
 git push --all origin -u

cd /home/username/Arduino
git init 
git remote add origin git@github.com:<user>/ArduinoProjects.git
git pull origin master
git push --all origin -u

cd /home/Arduino
git push

Make repository first at github (assuming local directoryname = reponame)

cd <reponame>
echo "# <reponame>" >> README.md
git init
git add README.md
git commit -m "first commit"
git remote add origin git@github.com:<user>/<reponame>.git
git push -u origin master