The way I manage this is described here.

Short description:

• the dotfiles repo is cloned as bare repo in ~/.dotfiles
• then you tell git that the work tree is your $HOME
• untracked files are simply ignored
• to track a file, simply add it to the repo
• to make this easier, an alias is used: alias config="git --git-dir=$HOME/.dotfiles --work-tree=$HOME"
• stage all changes with config add -u

git clone --bare https://github.com/janhieber/dotfiles.git .dotfiles
alias config="git --git-dir=$HOME/.dotfiles --work-tree=$HOME"
config checkout origin master