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To clone on a fresh install run the following (also available in clone.sh)

git clone --bare https://github.com/ash0x0/dotfiles.git $HOME/.dotfiles
function dotfiles {
   /usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME $@
}
mkdir -p .dotfiles-backup
dotfiles checkout
if [ $? = 0 ]; then
  echo "Checked out dotfiles.";
  else
    echo "Backing up pre-existing dot files.";
    dotfiles checkout 2>&1 | egrep "\s+\." | awk {'print $1'} | xargs -I{} mv {} .dotfiles-backup/{}
fi;
dotfiles checkout
dotfiles config status.showUntrackedFiles no

The above is sourced from the Bitbucket dotfiles tutorial