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